|
| Status |
Public on Mar 29, 2024 |
| Title |
homo_PFG_H3K27ac_input |
| Sample type |
SRA |
| |
|
| Source name |
hPSC_H1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hPSC_H1
Stage: PFG stage
genotype: ONECUT1e-664kb_homozygous_KO
treatment: input_control
|
| Growth protocol |
All differentiation experiments were performed on hESCs grown on vitronectin. hESCs were maintained in E8 medium for 2 days to reach ~80% confluence. hESCs were rinsed with 1X DPBS (without Mg2+ and Ca2+) and first differentiated into DE using S1/2 media, supplemented with 100 ng/ml Activin A (Bon Opus Biosciences) for three days and CHIR99021 (Stemgent, 04-0004-10) for two days (1st day, 5 µM; 2nd day, 0.5 µM). DE cells were rinsed with 1X DPBS (without Mg2+ and Ca2+) and then exposed to S1/2 media supplemented with 50 ng/ml of KGF (FGF7) (PeproTech, 100-19) and 0.25mM vitamin C (Sigma-Aldrich, A4544) for 2 days to reach GT stage. Cells were switched to S3/4 media supplemented with 50 ng/ml of FGF7, 0.25 mM vitamin C, and 1µM retinoic acid (RA) (Sigma-Aldrich, R2625) for 2 days to reach PFG stage.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked by formaldehyde and lysed by SDS lysis buffer. Sonicated nuclei were incubated with antibody overnight and then pulled down by dynabeads. After washing, decrosslinking was performed to isolate DNA.
aMPure XP size selection followed by KAPA HTP Library Preparation Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
bowtie 2 (2.5.1) alignment
MACS2 (2.2.9.1) peak calling to generate signal tracks
Assembly: hg38
Supplementary files format and content: Coverage track in bigWig format
|
| |
|
| Submission date |
Mar 12, 2024 |
| Last update date |
Mar 29, 2024 |
| Contact name |
Samuel Joseph Kaplan |
| Organization name |
Sloan Kettering Institute
|
| Department |
Developmental Biology Program
|
| Street address |
430 E 67th St
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE261392 |
CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant [H3K27ac_ChIP-seq] |
| GSE267330 |
CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant |
|
| Relations |
| BioSample |
SAMN40418727 |
| SRA |
SRX23911031 |
