SRX17998849 GSM6671106_r1 SRP404100 PRJNA893359 SRS15508568 GSM6671106 GSM6671106 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998850 GSM6671107_r1 SRP404100 PRJNA893359 SRS15508569 GSM6671107 GSM6671107 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998851 GSM6671108_r1 SRP404100 PRJNA893359 SRS15508570 GSM6671108 GSM6671108 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998852 GSM6671109_r1 SRP404100 PRJNA893359 SRS15508571 GSM6671109 GSM6671109 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998853 GSM6671110_r1 SRP404100 PRJNA893359 SRS15508572 GSM6671110 GSM6671110 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998854 GSM6671111_r1 SRP404100 PRJNA893359 SRS15508573 GSM6671111 GSM6671111 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998855 GSM6671112_r1 SRP404100 PRJNA893359 SRS15508574 GSM6671112 GSM6671112 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998856 GSM6671113_r1 SRP404100 PRJNA893359 SRS15508575 GSM6671113 GSM6671113 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998857 GSM6671097_r1 SRP404100 PRJNA893359 SRS15508576 GSM6671097 GSM6671097 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998858 GSM6671130_r1 SRP404100 PRJNA893359 SRS15508577 GSM6671130 GSM6671130 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998859 GSM6671131_r1 SRP404100 PRJNA893359 SRS15508578 GSM6671131 GSM6671131 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998860 GSM6671132_r1 SRP404100 PRJNA893359 SRS15508579 GSM6671132 GSM6671132 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998861 GSM6671134_r1 SRP404100 PRJNA893359 SRS15508580 GSM6671134 GSM6671134 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998862 GSM6671135_r1 SRP404100 PRJNA893359 SRS15508581 GSM6671135 GSM6671135 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998863 GSM6671133_r1 SRP404100 PRJNA893359 SRS15508582 GSM6671133 GSM6671133 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998864 GSM6671136_r1 SRP404100 PRJNA893359 SRS15508583 GSM6671136 GSM6671136 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998865 GSM6671137_r1 SRP404100 PRJNA893359 SRS15508584 GSM6671137 GSM6671137 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998866 GSM6671098_r1 SRP404100 PRJNA893359 SRS15508585 GSM6671098 GSM6671098 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998867 GSM6671099_r1 SRP404100 PRJNA893359 SRS15508586 GSM6671099 GSM6671099 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998868 GSM6671100_r1 SRP404100 PRJNA893359 SRS15508587 GSM6671100 GSM6671100 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998869 GSM6671101_r1 SRP404100 PRJNA893359 SRS15508589 GSM6671101 GSM6671101 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998870 GSM6671102_r1 SRP404100 PRJNA893359 SRS15508588 GSM6671102 GSM6671102 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998871 GSM6671103_r1 SRP404100 PRJNA893359 SRS15508590 GSM6671103 GSM6671103 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998872 GSM6671104_r1 SRP404100 PRJNA893359 SRS15508591 GSM6671104 GSM6671104 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998873 GSM6671105_r1 SRP404100 PRJNA893359 SRS15508592 GSM6671105 GSM6671105 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998874 GSM6671122_r1 SRP404100 PRJNA893359 SRS15508594 GSM6671122 GSM6671122 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998875 GSM6671123_r1 SRP404100 PRJNA893359 SRS15508593 GSM6671123 GSM6671123 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998876 GSM6671124_r1 SRP404100 PRJNA893359 SRS15508596 GSM6671124 GSM6671124 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998877 GSM6671125_r1 SRP404100 PRJNA893359 SRS15508595 GSM6671125 GSM6671125 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998878 GSM6671126_r1 SRP404100 PRJNA893359 SRS15508597 GSM6671126 GSM6671126 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998879 GSM6671127_r1 SRP404100 PRJNA893359 SRS15508598 GSM6671127 GSM6671127 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998880 GSM6671128_r1 SRP404100 PRJNA893359 SRS15508599 GSM6671128 GSM6671128 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998881 GSM6671129_r1 SRP404100 PRJNA893359 SRS15508600 GSM6671129 GSM6671129 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998882 GSM6671138_r1 SRP404100 PRJNA893359 SRS15508601 GSM6671138 GSM6671138 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998883 GSM6671139_r1 SRP404100 PRJNA893359 SRS15508602 GSM6671139 GSM6671139 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998884 GSM6671140_r1 SRP404100 PRJNA893359 SRS15508603 GSM6671140 GSM6671140 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998885 GSM6671141_r1 SRP404100 PRJNA893359 SRS15508604 GSM6671141 GSM6671141 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998886 GSM6671142_r1 SRP404100 PRJNA893359 SRS15508605 GSM6671142 GSM6671142 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998887 GSM6671143_r1 SRP404100 PRJNA893359 SRS15508606 GSM6671143 GSM6671143 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998888 GSM6671144_r1 SRP404100 PRJNA893359 SRS15508607 GSM6671144 GSM6671144 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998889 GSM6671145_r1 SRP404100 PRJNA893359 SRS15508608 GSM6671145 GSM6671145 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998890 GSM6671146_r1 SRP404100 PRJNA893359 SRS15508609 GSM6671146 GSM6671146 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998891 GSM6671147_r1 SRP404100 PRJNA893359 SRS15508610 GSM6671147 GSM6671147 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998892 GSM6671148_r1 SRP404100 PRJNA893359 SRS15508611 GSM6671148 GSM6671148 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998893 GSM6671149_r1 SRP404100 PRJNA893359 SRS15508612 GSM6671149 GSM6671149 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998894 GSM6671150_r1 SRP404100 PRJNA893359 SRS15508613 GSM6671150 GSM6671150 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998895 GSM6671151_r1 SRP404100 PRJNA893359 SRS15508614 GSM6671151 GSM6671151 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998896 GSM6671152_r1 SRP404100 PRJNA893359 SRS15508615 GSM6671152 GSM6671152 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998897 GSM6671114_r1 SRP404100 PRJNA893359 SRS15508616 GSM6671114 GSM6671114 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998898 GSM6671115_r1 SRP404100 PRJNA893359 SRS15508617 GSM6671115 GSM6671115 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998899 GSM6671116_r1 SRP404100 PRJNA893359 SRS15508618 GSM6671116 GSM6671116 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998900 GSM6671117_r1 SRP404100 PRJNA893359 SRS15508619 GSM6671117 GSM6671117 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998901 GSM6671118_r1 SRP404100 PRJNA893359 SRS15508620 GSM6671118 GSM6671118 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998902 GSM6671119_r1 SRP404100 PRJNA893359 SRS15508621 GSM6671119 GSM6671119 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998903 GSM6671120_r1 SRP404100 PRJNA893359 SRS15508622 GSM6671120 GSM6671120 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998904 GSM6671161_r1 SRP404100 PRJNA893359 SRS15508624 GSM6671161 GSM6671161 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998905 GSM6671162_r1 SRP404100 PRJNA893359 SRS15508623 GSM6671162 GSM6671162 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998906 GSM6671163_r1 SRP404100 PRJNA893359 SRS15508626 GSM6671163 GSM6671163 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998907 GSM6671164_r1 SRP404100 PRJNA893359 SRS15508625 GSM6671164 GSM6671164 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998908 GSM6671153_r1 SRP404100 PRJNA893359 SRS15508627 GSM6671153 GSM6671153 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998909 GSM6671154_r1 SRP404100 PRJNA893359 SRS15508628 GSM6671154 GSM6671154 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998910 GSM6671155_r1 SRP404100 PRJNA893359 SRS15508629 GSM6671155 GSM6671155 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998911 GSM6671156_r1 SRP404100 PRJNA893359 SRS15508630 GSM6671156 GSM6671156 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998912 GSM6671157_r1 SRP404100 PRJNA893359 SRS15508631 GSM6671157 GSM6671157 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998913 GSM6671158_r1 SRP404100 PRJNA893359 SRS15508632 GSM6671158 GSM6671158 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998914 GSM6671159_r1 SRP404100 PRJNA893359 SRS15508633 GSM6671159 GSM6671159 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998915 GSM6671160_r1 SRP404100 PRJNA893359 SRS15508634 GSM6671160 GSM6671160 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000 SRX17998916 GSM6671121_r1 SRP404100 PRJNA893359 SRS15508635 GSM6671121 GSM6671121 ATAC-seq GENOMIC other Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment. Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details. Illumina NovaSeq 6000