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| Status |
Public on Apr 24, 2022 |
| Title |
WT ATAC-seq replicate 6 |
| Sample type |
SRA |
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| Source name |
CD8+ T cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: CD8+ T cells
genotype: Wild type
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| Treatment protocol |
For c-Myc KO samples, Naïve CD8 T cells were treated with 4OHT for 24hr., and then activated by anti-CD3/28 with ICAM for 36hr. For Arid1a KO samples, Naïve CD8 T cells were activated by anti-CD3/28 with ICAM for 36hr., and then first-division CD8 T cells were sorted.
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| Growth protocol |
Naïve CD8 T cells were activated with anti-CD3/28 and ICAM for 36hr. First division Myc high and Myc low cells were sorted.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 cells were pelleted at 500 x g for 5 min at 4°C. Samples were washed in 1 ml cold PBS and resuspended in 50 ul cold cell lysis buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). Nuclei were pelleted at 1000 x g for 10 min and resuspended in 50 ml transposition reaction mixture (25 ml TD buffer, 2.5 ml TDE1, 22.5 ml ddH2O) (20034197, Illumina). Samples were incubated at 42°C for 45 min. DNA was then purified using MiniElute PCR Purification Kit (28004, Qiagen). Libraries were barcoded and amplified with Q5 High-Fidelity 2x Master Mix (M0492S, NEB).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Paired-end sequencing reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Reads were aligned to a hybrid genome of reference mouse mm10 assembly and drosophila Ensembl r97 using Bowtie 2 (version 2.3.5.1) with settings --end-to-end --very-sensitive -X 2000.
The BAM file was filtered with SAMtools (version 1.9), BamTools (version 2.5.1) and scripts of nf-core/chipseq 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; only reads mapped in proper pair were kept (-F 1804 -f 2 -q 30).
Peaks were called using MACS (version 2.1.2) with narrowPeak setting, --extsize 200, and recommended mappable genome size (default value for other parameters).
Chromatin accessibility signal was normalized by scaling to 1 million mapped reads using BEDTools (version 2.27.1) and bedGraphToBigWig (version 377) with default parameters. For Myc KO vs wild type (WT replicate 4-6), it was scaled to 1 million reads mapped to spike-in drosophila genome.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files scaling tag count to 1 million mapped reads or 1 million mapped reads of spike-in genome.
Supplementary_files_format_and_content: Bed files of peaks called using MACS2
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| Submission date |
Sep 07, 2021 |
| Last update date |
Apr 26, 2022 |
| Contact name |
Douglas R Green |
| E-mail(s) |
douglas.green@stjude.org
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| Organization name |
St Jude Children's Research Hospital
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| Department |
Immunology
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| Lab |
Green lab
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| Street address |
262 Danny Thomas Pl
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| City |
Memphis |
| State/province |
United States |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE183618 |
BAF complex cooperates with c-Myc to orchestrate early fate decisions of CD8 T cells (ATAC II) |
| GSE183619 |
BAF complex cooperates with c-Myc to orchestrate early fate decisions of CD8 T cells |
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| Relations |
| BioSample |
SAMN21326631 |
| SRA |
SRX12036037 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5563563_WT.ATAC.rep6.bed.gz |
1.8 Mb |
(ftp)(http) |
BED |
| GSM5563563_WT.ATAC.rep6.bigWig |
704.1 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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