ERS6469203 SAMEA8784841 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784841 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:hypothalamic neuron day12 rep1 broker name ArrayExpress cell line iPSC derived cell line cell type early hypothalamic neuron common name human day of differentiation 12 developmental stage embryo stage genotype wild type genotype organism part hypothalamus replicate 1 sample name E-MTAB-10488:hypothalamic neuron day12 rep1 ERS6469204 SAMEA8784842 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784842 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:hypothalamic neuron day12 rep2 broker name ArrayExpress cell line iPSC derived cell line cell type early hypothalamic neuron common name human day of differentiation 12 developmental stage embryo stage genotype wild type genotype organism part hypothalamus replicate 2 sample name E-MTAB-10488:hypothalamic neuron day12 rep2 ERS6469205 SAMEA8784843 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784843 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:hypothalamic neuron day16 rep1 broker name ArrayExpress cell line iPSC derived cell line cell type mid hypothalamic neuron common name human day of differentiation 16 developmental stage embryo stage genotype wild type genotype organism part hypothalamus replicate 1 sample name E-MTAB-10488:hypothalamic neuron day16 rep1 ERS6469206 SAMEA8784844 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784844 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:hypothalamic neuron day16 rep2 broker name ArrayExpress cell line iPSC derived cell line cell type mid hypothalamic neuron common name human day of differentiation 16 developmental stage embryo stage genotype wild type genotype organism part hypothalamus replicate 2 sample name E-MTAB-10488:hypothalamic neuron day16 rep2 ERS6469207 SAMEA8784845 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784845 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:hypothalamic neuron day27 rep1 broker name ArrayExpress cell line iPSC derived cell line cell type mature hypothalamic neuron common name human day of differentiation 27 developmental stage embryo stage genotype wild type genotype organism part hypothalamus replicate 1 sample name E-MTAB-10488:hypothalamic neuron day27 rep1 ERS6469208 SAMEA8784846 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784846 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:hypothalamic neuron day27 rep2 broker name ArrayExpress cell line iPSC derived cell line cell type mature hypothalamic neuron common name human day of differentiation 27 developmental stage embryo stage genotype wild type genotype organism part hypothalamus replicate 2 sample name E-MTAB-10488:hypothalamic neuron day27 rep2 ERS6469209 SAMEA8784847 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784847 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:SGBS day0 rep1 broker name ArrayExpress cell line SGBS cell type preadipocyte common name human day of differentiation 0 developmental stage embryo stage disease Simpson-Golabi-Behmel syndrome genotype wild type genotype organism part adipose tissue replicate 1 sample name E-MTAB-10488:SGBS day0 rep1 ERS6469210 SAMEA8784848 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784848 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:SGBS day0 rep2 broker name ArrayExpress cell line SGBS cell type preadipocyte common name human day of differentiation 0 developmental stage embryo stage disease Simpson-Golabi-Behmel syndrome genotype wild type genotype organism part adipose tissue replicate 2 sample name E-MTAB-10488:SGBS day0 rep2 ERS6469211 SAMEA8784849 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784849 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:SGBS day16 rep1 broker name ArrayExpress cell line SGBS cell type small adipocyte common name human day of differentiation 16 developmental stage embryo stage disease Simpson-Golabi-Behmel syndrome genotype wild type genotype organism part adipose tissue replicate 1 sample name E-MTAB-10488:SGBS day16 rep1 ERS6469212 SAMEA8784850 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784850 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:SGBS day16 rep2 broker name ArrayExpress cell line SGBS cell type small adipocyte common name human day of differentiation 16 developmental stage embryo stage disease Simpson-Golabi-Behmel syndrome genotype wild type genotype organism part adipose tissue replicate 2 sample name E-MTAB-10488:SGBS day16 rep2 ERS6469213 SAMEA8784851 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784851 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:SGBS day2 rep1 broker name ArrayExpress cell line SGBS cell type preadipocyte common name human day of differentiation 2 developmental stage embryo stage disease Simpson-Golabi-Behmel syndrome genotype wild type genotype organism part adipose tissue replicate 1 sample name E-MTAB-10488:SGBS day2 rep1 ERS6469214 SAMEA8784852 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784852 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:SGBS day2 rep2 broker name ArrayExpress cell line SGBS cell type preadipocyte common name human day of differentiation 2 developmental stage embryo stage disease Simpson-Golabi-Behmel syndrome genotype wild type genotype organism part adipose tissue replicate 2 sample name E-MTAB-10488:SGBS day2 rep2 ERS6469215 SAMEA8784853 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784853 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:SGBS day8 rep1 broker name ArrayExpress cell line SGBS cell type small adipocyte common name human day of differentiation 8 developmental stage embryo stage disease Simpson-Golabi-Behmel syndrome genotype wild type genotype organism part adipose tissue replicate 1 sample name E-MTAB-10488:SGBS day8 rep1 ERS6469216 SAMEA8784854 9606 Homo sapiens Protocols: In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing. See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene. ENA first public 2021-05-29 ENA last update 2021-05-29 External Id SAMEA8784854 INSDC center alias UNIVERSITY OF CHICAGO INSDC center name UNIVERSITY OF CHICAGO INSDC first public 2021-05-29T00:13:48Z INSDC last update 2021-05-29T00:13:48Z INSDC status public Submitter Id E-MTAB-10488:SGBS day8 rep2 broker name ArrayExpress cell line SGBS cell type small adipocyte common name human day of differentiation 8 developmental stage embryo stage disease Simpson-Golabi-Behmel syndrome genotype wild type genotype organism part adipose tissue replicate 2 sample name E-MTAB-10488:SGBS day8 rep2