ERS2657608 SAMEA4837741 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:18Z External Id SAMEA4837741 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:18Z INSDC status public Submitter Id E-MTAB-6701:FCA7167219 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45+ individual D6 organism part decidua run FCA7167219 sample name E-MTAB-6701:FCA7167219 scientific_name Homo sapiens sex female ERS2657610 SAMEA4837743 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:18Z External Id SAMEA4837743 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:18Z INSDC status public Submitter Id E-MTAB-6701:FCA7167221 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45+ individual D7 organism part decidua run FCA7167221 sample name E-MTAB-6701:FCA7167221 scientific_name Homo sapiens sex female ERS2657611 SAMEA4837744 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837744 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7167222 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45- individual D7 organism part decidua run FCA7167222 sample name E-MTAB-6701:FCA7167222 scientific_name Homo sapiens sex female ERS2657612 SAMEA4837745 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837745 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7167223 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45+ individual D6 organism part decidua run FCA7167223 sample name E-MTAB-6701:FCA7167223 scientific_name Homo sapiens sex female ERS2657613 SAMEA4837746 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837746 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7167224 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45- individual D6 organism part decidua run FCA7167224 sample name E-MTAB-6701:FCA7167224 scientific_name Homo sapiens sex female ERS2657614 SAMEA4837747 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837747 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7167226 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45- individual D7 organism part decidua run FCA7167226 sample name E-MTAB-6701:FCA7167226 scientific_name Homo sapiens sex female ERS2657618 SAMEA4837751 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837751 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7167230 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker PB individual D7 organism part blood run FCA7167230 sample name E-MTAB-6701:FCA7167230 scientific_name Homo sapiens sex female ERS2657619 SAMEA4837752 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837752 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7167231 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker PB individual D6 organism part blood run FCA7167231 sample name E-MTAB-6701:FCA7167231 scientific_name Homo sapiens sex female ERS2657620 SAMEA4837753 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837753 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7167232 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker PB individual D6 organism part blood run FCA7167232 sample name E-MTAB-6701:FCA7167232 scientific_name Homo sapiens sex female ERS2657621 SAMEA4837754 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837754 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7196218 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45+ individual D8 organism part decidua run FCA7196218 sample name E-MTAB-6701:FCA7196218 scientific_name Homo sapiens sex female ERS2657622 SAMEA4837755 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837755 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7196219 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45- individual D8 organism part decidua run FCA7196219 sample name E-MTAB-6701:FCA7196219 scientific_name Homo sapiens sex female ERS2657623 SAMEA4837756 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837756 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7196220 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker all individual D8 organism part placenta run FCA7196220 sample name E-MTAB-6701:FCA7196220 scientific_name Homo sapiens sex female ERS2657624 SAMEA4837757 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837757 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7196224 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45+ individual D9 organism part decidua run FCA7196224 sample name E-MTAB-6701:FCA7196224 scientific_name Homo sapiens sex female ERS2657625 SAMEA4837758 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837758 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7196225 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45- individual D9 organism part decidua run FCA7196225 sample name E-MTAB-6701:FCA7196225 scientific_name Homo sapiens sex female ERS2657626 SAMEA4837759 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837759 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7196226 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker all individual D9 organism part placenta run FCA7196226 sample name E-MTAB-6701:FCA7196226 scientific_name Homo sapiens sex female ERS2657627 SAMEA4837760 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837760 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7196229 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker PB individual D9 organism part blood run FCA7196229 sample name E-MTAB-6701:FCA7196229 scientific_name Homo sapiens sex female ERS2657628 SAMEA4837761 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837761 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7196231 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker PB individual D8 organism part blood run FCA7196231 sample name E-MTAB-6701:FCA7196231 scientific_name Homo sapiens sex female ERS2657629 SAMEA4837762 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837762 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7474062 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45+ individual D10 organism part decidua run FCA7474062 sample name E-MTAB-6701:FCA7474062 scientific_name Homo sapiens sex female ERS2657630 SAMEA4837763 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837763 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7474063 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45- individual D10 organism part decidua run FCA7474063 sample name E-MTAB-6701:FCA7474063 scientific_name Homo sapiens sex female ERS2657631 SAMEA4837764 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837764 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7474064 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker all individual D10 organism part placenta run FCA7474064 sample name E-MTAB-6701:FCA7474064 scientific_name Homo sapiens sex female ERS2657632 SAMEA4837765 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837765 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7474065 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker all individual D10 organism part placenta run FCA7474065 sample name E-MTAB-6701:FCA7474065 scientific_name Homo sapiens sex female ERS2657633 SAMEA4837766 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837766 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7474066 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker Epcam+ individual D10 organism part placenta run FCA7474066 sample name E-MTAB-6701:FCA7474066 scientific_name Homo sapiens sex female ERS2657635 SAMEA4837768 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837768 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7474068 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker all individual D11 organism part placenta run FCA7474068 sample name E-MTAB-6701:FCA7474068 scientific_name Homo sapiens sex female ERS2657636 SAMEA4837769 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837769 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7474069 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker Epcam+ individual D11 organism part placenta run FCA7474069 sample name E-MTAB-6701:FCA7474069 scientific_name Homo sapiens sex female ERS2657637 SAMEA4837770 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837770 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7511881 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45+ individual D12 organism part decidua run FCA7511881 sample name E-MTAB-6701:FCA7511881 scientific_name Homo sapiens sex female ERS2657638 SAMEA4837771 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837771 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7511882 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker CD45- individual D12 organism part decidua run FCA7511882 sample name E-MTAB-6701:FCA7511882 scientific_name Homo sapiens sex female ERS2657639 SAMEA4837772 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837772 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7511883 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker HLAG+ individual D12 organism part decidua run FCA7511883 sample name E-MTAB-6701:FCA7511883 scientific_name Homo sapiens sex female ERS2657640 SAMEA4837773 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837773 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7511884 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker all individual D12 organism part placenta run FCA7511884 sample name E-MTAB-6701:FCA7511884 scientific_name Homo sapiens sex female ERS2657641 SAMEA4837774 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837774 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7511885 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker HLAG+ individual D12 organism part placenta run FCA7511885 sample name E-MTAB-6701:FCA7511885 scientific_name Homo sapiens sex female ERS2657642 SAMEA4837775 9606 Homo sapiens Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke's Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing.Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min.Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel (Fig xxx) designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7).For the droplet RNA-seq methods, blood and decidual cells were sorted into immune (CD45+) and non-immune (CD45-) fractions. Only viable cells were considered, and B cells (CD19+/CD20+) cells were excluded from our analysis. Placental cells were stained for DAPI and only viable cells were sorted. Cells were sorted into an eppendorf containing PBS with 0.04% BSA. Cells were immediately counted using a Neubauer hemocytometer and loaded in the 10x-genomics machine. RNA was converted into cDNA and amplified as part of the 10x v2 chemistry. Libraries were constructed using the 10x v2 chemistry ENA-FIRST-PUBLIC 2018-10-02T17:04:10Z ENA-LAST-UPDATE 2018-08-17T18:36:19Z External Id SAMEA4837775 INSDC center name Wellcome Sanger Institute INSDC first public 2018-10-02T17:04:10Z INSDC last update 2018-08-17T18:36:19Z INSDC status public Submitter Id E-MTAB-6701:FCA7511886 broker name ArrayExpress clinical information 6 to 12 weeks gestation common name human developmental stage adult disease normal facs marker Epcam+ individual D12 organism part placenta run FCA7511886 sample name E-MTAB-6701:FCA7511886 scientific_name Homo sapiens sex female