|
| Status |
Public on Jun 06, 2021 |
| Title |
ATAC_E7_ACT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
RUES2 human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RUES2
cell type: human embryonic stem cells
treatment with cpi: untreated
time point: 48 h
|
| Treatment protocol |
hESCs were treated with or without Wnt3a (100 ng/mL) +/- CPI-203 (1 µM) on day 1 and with or without Activin A (10 ng/mL) on day 2. Samples were collected after day 1 or day 2.
|
| Growth protocol |
RUES2 human embryonic stem cells grown (hESCs) in TeSR E7 media + rock inhibitor.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ATAC-seq samples, cells were collected and lysis of the outer membrane was carried out on ice. Nuclei were treated with Tn5 transposase for 30 minutes at 37 C.
For ATAC-seq samples, libraries were prepared from 10 µL of transposed DNA per sample with 10-11 cycles of PCR amplification.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
replicate 1
ATAC_Peak_Location_combined.txt
|
| Data processing |
RNAseq data were aligned to hg38 using Rsubread and the read counts associated with each gene were analyzed by featureCounts.
Fold changes relative to E7 were obtained using DESeq2.
ATAC-seq data were aligned to hg19 using bowtie2 and visualized using deepTools bamCoverage function.
Peaks were identified using MACS2 narrow peak calling. The area underneath each peak was calculated using the MultiCovBed function.
Genome_build: hg38 (GRCh38) or hg19 (GRCh37)
Supplementary_files_format_and_content: RNA-seq: Feature counts text files for both replicates.
Supplementary_files_format_and_content: ATAC-seq: Individual peak files (.bw) and combined peaks text file (all peaks in both replicates).
|
| |
|
| Submission date |
Jun 05, 2021 |
| Last update date |
Jun 06, 2021 |
| Contact name |
Anna Yoney |
| E-mail(s) |
ay2520@cumc.columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Genetics and Development
|
| Street address |
701 W 168th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE176222 |
RNA- and ATAC-seq data from hESCs differentiated with Wnt and Activin with or without CPI-203 |
|
| Relations |
| BioSample |
SAMN19580838 |
| SRA |
SRX11075301 |
