|
| Status |
Public on Apr 28, 2024 |
| Title |
KO1_DE |
| Sample type |
SRA |
| |
|
| Source name |
definitive endoderm
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H7
genotype: FOXA2 Knock-out
foxa2 protein: null
|
| Treatment protocol |
hESCs were differentiated to DE using PSC Definitive Endoderm Induction Kit (Thermo Fisher, A3062601).
hESCs were differentiated to APS and DE with a two-day protocol using PSC Definitive Endoderm Induction Kit (Thermo Fisher, A3062601) or following the protocol in the report (Loh et al., 2014)
|
| Growth protocol |
H7 hESCs (WiCell, WAe007-A) were cultured on plates pre-coated with 1% (v/v) Geltrex (Thermo Fisher, A1413302) with complete Essential 8 medium (Thermo Fisher, A1517001). Accutase (Thermo Fisher, A1110501) was used for cell dispersion and ROCK inhibitor Thiazovivin at 2 μΜ final concentration was used in the culture medium for the first day after re-plating cells.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol following the manufacturer’s instructions
RNA library was generated using the Solexa rapid library protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Homozygote FOXA2 Knock-out clone #1 differentiated to definitive endoderm
|
| Data processing |
Base-calling performed with CASAVA
RNA-Seq reads quality control performed with FastQC (version 0.10.1)
RNA-Seq reads were aligned to the hg38 genome assembly using STAR RNA-Seq aligner (version 2.7) with the following options: --outSJfilterReads Unique --outFilterMultimapNmax 1 --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif
We used Samtools (version 1.9) to convert STAR output .sam files into .bam files, and to sort and index them
We used HTSeq (version 0.11.1) to count how many reads overlapped an annotated gene (GENECODE v32 annotations) with the following options: htseq-count --stranded=no -f bam --additional-attr=gene_name -m union)
BigWig coverage files were generated with deepTools (version 2.4.1) with the following configurations: bamCoverage -of bigwig --binSize 50 --normalizeTo1x 2913022398 --ignoreDuplicates
Assembly: hg38
Supplementary files format and content: bigWig files containing the number of reads per 50 bp bins normalized to 1x sequencing depth (Reads Per Genomic Content)
Supplementary files format and content: text files containing the output of HTSeq, i.e. read counts in each annotated Ensemble gene (GENECODE v32 annotations)
|
| |
|
| Submission date |
May 23, 2022 |
| Last update date |
Apr 28, 2024 |
| Contact name |
Wulan Deng |
| E-mail(s) |
denglabpku@outlook.com
|
| Organization name |
Peking University
|
| Department |
BIOPIC
|
| Street address |
Beijing Haidian District Yiheyuan Road #5
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE203640 |
Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [RNA-seq] |
| GSE203650 |
Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells |
|
| Relations |
| BioSample |
SAMN28608480 |
| SRA |
SRX15426407 |
