|
| Status |
Public on Apr 24, 2022 |
| Title |
1st division Arid1a KO - IgG control |
| Sample type |
SRA |
| |
|
| Source name |
CD8+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD8+ T cells
genotype: Arid1a KO
|
| Treatment protocol |
For c-Myc KO samples, Naïve CD8 T cells were treated with 4OHT for 24hr before activation.
|
| Growth protocol |
Naïve CD8 T cells were activated with anti-CD3/28 and ICAM for 36hr. First division CD 8 T cells were sorted.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN ChIP-seq experiments were performed as previously described (Meers et al. Improved CUT&RUN chromatin profiling tools. eLife 8, e46314 (2019)) with slight modifications.
CUT&RUN
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end sequencing reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Reads were aligned to a hybrid reference of mouse mm10 and E. coli ASM584v2 using Bowtie 2 (version 2.3.5.1) with settings --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
The BAM file was filtered with SAMtools (version 1.9), BamTools (version 2.5.1) and scripts of nf-core/chipseq6 to discard reads, mates that were unmapped, or PCR/optical duplicates, or not primary alignments, or mapped to multiple locations, or mapped to ENCODE blacklisted regions, or have more than 4 mismatches (-F 0x004 -F 0x008 -F 0x0100 -F 0x0400 -f 0x001 -q 1).
MACS (version 2.1.2) was used to call peaks from the BAM file with IgG control and recommended mappable genome size (default value for other parameters). NarrowPeak mode was used for Myc, broadPeak mode for Arid1a and Brg1.
Signal was normalized by scaling to 1 million mapped reads using BEDTools (version 2.27.1) and bedGraphToBigWig (version 377) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files scaling tag count to 1 million mapped reads.
Supplementary_files_format_and_content: Bed files of peaks called using MACS2.
|
| |
|
| Submission date |
Sep 07, 2021 |
| Last update date |
Apr 26, 2022 |
| Contact name |
Douglas R Green |
| E-mail(s) |
douglas.green@stjude.org
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Immunology
|
| Lab |
Green lab
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
United States |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE183617 |
BAF complex cooperates with c-Myc to orchestrate early fate decisions of CD8 T cells (Cut&Run) |
| GSE183619 |
BAF complex cooperates with c-Myc to orchestrate early fate decisions of CD8 T cells |
|
| Relations |
| BioSample |
SAMN21326529 |
| SRA |
SRX12036062 |
