|
| Status |
Public on Nov 02, 2023 |
| Title |
mESC_WT_ATAC-seq_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: F121-9 wt mESCs
treatment: Untreated
assay: ATAC-seq
|
| Growth protocol |
Cells were grown in serum-free ES media supplemented with glutamine (Gibco), monothioglycerol (Sigma), MEK inhibitor (Reprocell), GSK3 inhibitor (Reprocell) and LIF (Cell Guidance Systems). Cells were passaged onto new gelatin-coated plates every other day, and received fresh media on other days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Harvested cells were resuspended in 50µL CSK Lysis Buffer (10 mM PIPES, pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton-X-100), incubated on ice for 5 min, and centrifuged for 5 min at 500 ´ g and 4ºC.
Samples were tagmented for 30 min at 37ºC using TDE1 Tagment DNA Enzyme (Illumina).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT 4
|
| Data processing |
Reads were trimmed for a minimum quality score of 20 using a custom script (https://github.com/AdelmanLab/NIH_scripts/tree/main/trim_and_filter_PE), adapter sequences were removed using cutadapt version 1.14.
Data was mapped to mm10 using bowtie 1.2.2
Bedgraphs were generated in 50bp bins from dedpulicated SAM files.
Assembly: mm10
Supplementary files format and content: All files with the .bw suffix are normalized BigWig files containing combined data from all replicates of the indicated treatment condition.
|
| |
|
| Submission date |
Mar 12, 2022 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Karen Adelman |
| E-mail(s) |
karen_adelman@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Biological Chemistry and Molecular Pharmacology
|
| Street address |
45 Shattuck St. LHRRB-201a
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE198517 |
Inhibition of SWI/SNF broadly disrupts enhancers and reveals remodeler redundancy at promoters |
|
| Relations |
| BioSample |
SAMN26631516 |
| SRA |
SRX14450321 |
