NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8141934 Query DataSets for GSM8141934
Status Public on Mar 29, 2024
Title Homo_PFG_RNAseq_rep1
Sample type SRA
 
Source name hPSC_H1
Organism Homo sapiens
Characteristics cell line: hPSC_H1
genotype: ONECUT1e-664kb_homozygous_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_homo_PFG_2_IGO_13401_B_7_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 SAMN40414310
SRA SRX23908372

Supplementary file Size Download File type/resource
GSM8141934_Homo_PFG_rep1_FwdStrand_ONECUT1-antisense.bw 50.9 Mb (ftp)(http) BW
GSM8141934_Homo_PFG_rep1_RevStrand_ONECUT1-sense.bw 48.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap