SRX2404787 GSM2420052 SRP094763 PRJNA356733 SRS1843995 SAMN06122633 ChIP-Seq GENOMIC ChIP KIT positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420052 GSM2420052 GEO Accession GSM2420052 SRX2404788 GSM2420053 SRP094763 PRJNA356733 SRS1843996 SAMN06122632 ChIP-Seq GENOMIC ChIP KIT positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420053 GSM2420053 GEO Accession GSM2420053 SRX2404789 GSM2420054 SRP094763 PRJNA356733 SRS1843997 SAMN06122631 ChIP-Seq GENOMIC ChIP SSEA1 and INTEGRINβ-3 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420054 GSM2420054 GEO Accession GSM2420054 SRX2404790 GSM2420055 SRP094763 PRJNA356733 SRS1843998 SAMN06122630 ChIP-Seq GENOMIC ChIP SSEA1 and INTEGRINβ-3 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420055 GSM2420055 GEO Accession GSM2420055 SRX2404791 GSM2420056 SRP094763 PRJNA356733 SRS1843999 SAMN06122629 ChIP-Seq GENOMIC ChIP EGFP-BLIMP1 embryos were obtained with intracytoplasmic sperm injection (ICSI) to oocytes (Kimura, 1995 #3053) and transfer of two-cell-stage embryos into oviducts of the surrogate mother mice. The embryonic male gonads at E12.5 were collected, for which sex was determined with the morphological features, and dissociated into single cells by incubating with 0.05 % trypsin and 0.5 mM EDTA (GIBCO) in PBS at 37 °C for 5 min. The cell suspension was then incubated with mouse anti-SSEA1 antibody conjugated with Alexa Fluor 647 (BioLegend). SSEA1 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420056 GSM2420056 GEO Accession GSM2420056 SRX2404792 GSM2420057 SRP094763 PRJNA356733 SRS1844000 SAMN06122628 ChIP-Seq GENOMIC ChIP EGFP-BLIMP1 embryos were obtained with intracytoplasmic sperm injection (ICSI) to oocytes (Kimura, 1995 #3053) and transfer of two-cell-stage embryos into oviducts of the surrogate mother mice. The embryonic female gonads at E12.5 were collected, for which sex was determined with the morphological features, and dissociated into single cells by incubating with 0.05 % trypsin and 0.5 mM EDTA (GIBCO) in PBS at 37 °C for 5 min. The cell suspension was then incubated with mouse anti-SSEA1 antibody conjugated with Alexa Fluor 647 (BioLegend). SSEA1 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420057 GSM2420057 GEO Accession GSM2420057 SRX2404793 GSM2420058 SRP094763 PRJNA356733 SRS1844001 SAMN06122627 ChIP-Seq GENOMIC ChIP Intestinal epithelium were isolated as described (Gracz et al., 2012) with minor modifications. The intestine (E16.5) from caudal half of duodenum to the ileocecal junction of EGFP-BLIMP1 mice were dissected, and the surrounding connective tissues and vessels were gently removed. The isolated intestine were placed in the 1.5 ml eppendorf tube containing ice-cold PBS and cut into small pieces as fine as possible. The intestine fragments were then transferred to 10 ml Falcon tube containing dissociation reagent ♯1 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA, 75 μL of 1 M (1.5 mM) DTT] and placed on ice for 20min. After the incubation, dissociation reagent ♯1 was replaced with dissociation reagent ♯2 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA]. After 10 min incubation at 37 °C, the tube that contained intestine was shaken by hand for 30 sec to release epithelium from the basement membrane. Dissociated cells were washed by removing supernatant and re-suspending cells in 10 mL PBS with 10% FBS. The cells were collected by centrifugation and then re-suspended in 10 mL DMEM containing 8-mg Dispase (GIBCO), which digested cell–cell junction proteins and dissociated the whole epithelium to single cells. The cells were then incubated in a water bath for 10 min at 37°C with vigorous shaking every 2 min. After adding 10 % FBS, the cell suspension was passed through the cell strainer to remove large undissociated clumps of cells and connective tissues. BLIMP1 and EpCAM positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420058 GSM2420058 GEO Accession GSM2420058 SRX2404794 GSM2420059 SRP094763 PRJNA356733 SRS1844002 SAMN06122626 ChIP-Seq GENOMIC ChIP Intestinal epithelium were isolated as described (Gracz et al., 2012) with minor modifications. The intestine (E16.5) from caudal half of duodenum to the ileocecal junction of EGFP-BLIMP1 mice were dissected, and the surrounding connective tissues and vessels were gently removed. The isolated intestine were placed in the 1.5 ml eppendorf tube containing ice-cold PBS and cut into small pieces as fine as possible. The intestine fragments were then transferred to 10 ml Falcon tube containing dissociation reagent ♯1 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA, 75 μL of 1 M (1.5 mM) DTT] and placed on ice for 20min. After the incubation, dissociation reagent ♯1 was replaced with dissociation reagent ♯2 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA]. After 10 min incubation at 37 °C, the tube that contained intestine was shaken by hand for 30 sec to release epithelium from the basement membrane. Dissociated cells were washed by removing supernatant and re-suspending cells in 10 mL PBS with 10% FBS. The cells were collected by centrifugation and then re-suspended in 10 mL DMEM containing 8-mg Dispase (GIBCO), which digested cell–cell junction proteins and dissociated the whole epithelium to single cells. The cells were then incubated in a water bath for 10 min at 37°C with vigorous shaking every 2 min. After adding 10 % FBS, the cell suspension was passed through the cell strainer to remove large undissociated clumps of cells and connective tissues. BLIMP1 and EpCAM positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420059 GSM2420059 GEO Accession GSM2420059 SRX2404795 GSM2420060 SRP094763 PRJNA356733 SRS1844003 SAMN06122625 ChIP-Seq GENOMIC ChIP Retinal tissues (P4) were dissociated from eye balls of EGFP-BLIMP1 mice and the incubation with 0.1 % trypsin and 1 mM EDTA in PBS at 37 °C for 10 min. Trypsin was then inactivated by adding equal volume of PBS/10% FBS supplemented with 0.1mg/mL DNaseI (Sigma). BLIMP1 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420060 GSM2420060 GEO Accession GSM2420060 SRX2404796 GSM2420061 SRP094763 PRJNA356733 SRS1844004 SAMN06122624 ChIP-Seq GENOMIC ChIP Retinal tissues (P4) were dissociated from eye balls of EGFP-BLIMP1 mice and the incubation with 0.1 % trypsin and 1 mM EDTA in PBS at 37 °C for 10 min. Trypsin was then inactivated by adding equal volume of PBS/10% FBS supplemented with 0.1mg/mL DNaseI (Sigma). BLIMP1 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420061 GSM2420061 GEO Accession GSM2420061 SRX2404797 GSM2420062 SRP094763 PRJNA356733 SRS1844005 SAMN06122623 ChIP-Seq GENOMIC ChIP After 3 days of stimulation, cells were harvested and incubated with rat anti-CD138 (Syndecan-1) antibody conjugated with APC. BLIMP1 and CD138 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420062 GSM2420062 GEO Accession GSM2420062 SRX2404798 GSM2420063 SRP094763 PRJNA356733 SRS1844006 SAMN06122622 ChIP-Seq GENOMIC ChIP After 3 days of stimulation, cells were harvested and incubated with rat anti-CD138 (Syndecan-1) antibody conjugated with APC. BLIMP1 and CD138 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420063 GSM2420063 GEO Accession GSM2420063 SRX2404799 GSM2420064 SRP094763 PRJNA356733 SRS1844007 SAMN06122621 ChIP-Seq GENOMIC ChIP EGFP-BLIMP1 embryos were obtained with intracytoplasmic sperm injection (ICSI) to oocytes (Kimura, 1995 #3053) and transfer of two-cell-stage embryos into oviducts of the surrogate mother mice. The embryonic male gonads at E12.5 were collected, for which sex was determined with the morphological features, and dissociated into single cells by incubating with 0.05 % trypsin and 0.5 mM EDTA (GIBCO) in PBS at 37 °C for 5 min. The cell suspension was then incubated with mouse anti-SSEA1 antibody conjugated with Alexa Fluor 647 (BioLegend). SSEA1 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015). Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction. Illumina HiSeq 2500 gds 302420064 GSM2420064 GEO Accession GSM2420064