|
| Status |
Public on Mar 29, 2024 |
| Title |
Het2_PFG_RNAseq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
hPSC_H1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hPSC_H1
genotype: ONECUT1e-664kb_heterozygous_KO
Stage: PFG stage
|
| 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 |
total RNA |
| Extraction protocol |
Cells were frozen and total RNA extracted with the Zymo Quick-RNA MiniPrep kit.
Illumina TruSeq Stranded Total RNA LT Kit (RS-122-1202)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample_het2_PFG_2_IGO_13401_B_6_R1.fastq.gz_wt-het-homo_GT_PFG_raw_counts.txt
|
| Data processing |
STAR alignment
Featurecounts quantification
*.bw data was generated using samtools to split aligned reads by strand, followed by generating *.bw using scale factors calculated on unsplit .bam files.
Assembly: hg38
Supplementary files format and content: Raw count table
Supplementary files format and content: bigwig
|
| |
|
| 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) |
| GSE261390 |
CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant [RNA-seq] |
| GSE267330 |
CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant |
|
| Relations |
| BioSample |
SAMN40414316 |
| SRA |
SRX23908366 |
