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| Status |
Public on Aug 01, 2024 |
| Title |
CD8 T AclyKO bio rep 3 |
| 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: Acly f/f Cd4Cre+
treatment: Vehicle (DMSO)
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| Growth protocol |
Isolated CD8 T cells were activated in VIM media with plate bound CD3/CD28 and IL-2 for 48 hours in the presence or absence of Acss2 inhibitor or acetate.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed according to Grandi et al 2022. Transposition was done for 45 mins at 37C mixing at 800rpm.
Library quantification and amplification was performed according to Grandi et al 2022. Using the full DNA output for each sample from ATAC libraries were initially amplified for 5 cycles. qPCR on part of these amplfied libraries was used to determine the number of additional cycles of amplification (+9 cycles). Post amplification libraries were size selected using AMPure XP beads from Beckman Coulter (0.6x for upper cutoff and 1.2x for lower cutoff). Libraries were validated using the Agilent High Sensitivity DNA Kit.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Isolated CD8 T cells were activated in VIM media with plate bound CD3/CD28 and IL-2 for 48 hours in the presence or absence of Acss2 inhibitor or acetate.
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| Data processing |
Reads were trimmed using TrimGalore v0.6.10 (Krueger et al., 2021) in paired-end mode with default parameters then aligned to the mm10 genome using ‘bwa mem’ v0.7.17 (Li, 2013), marking duplicate reads using SAMBLASTER v0.1.26 (Faust & Hall, 2014). For peak calling and differential accessibility analysis, alignments were quality-filtered, including removal of mitochondrial alignments, then deduplicated using ‘samtools view’ v1.17 (Li et al., 2009), with the parameters ‘-q 30 -F 2828 -f 2’ and ’-F 1024’ respectively. To call peaks centered at cut sites, BAM files were converted to BEDPE format using ‘bedtools bamtobed’ v2.30.0 (Quinlan & Hall, 2010), with the parameters ‘-bedpe -mate1’ followed by an AWK command to convert the resulting BEDPE file to BED format; ‘macs2 callpeak’ v2.2.7.1 (Zhang et al., 2008) was used with the parameters, ‘--keep-dup “all” -g mm -f “BED” --shift -75 --extsize 150 --nomodel --call-summits -B --SPMR’. Output bedgraph files were converted to BigWig format using bedGraphToBigWig from UCSCtools.
Assembly: mm10
Supplementary files format and content: BigWig, library size normalized read coverage centered at cut sites
Supplementary files format and content: NarrowPeak, peaks called by MACS2
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| Submission date |
Mar 30, 2024 |
| Last update date |
Aug 01, 2024 |
| Contact name |
Russell Jones |
| E-mail(s) |
russell.jones@vai.org
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| Phone |
6162345299
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| Organization name |
Van Andel Institute
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| Street address |
333 Bostwick Ave. NE
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| City |
Grand Rapids |
| State/province |
Michigan |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE262865 |
ACSS2 and ACLY link nutrient-dependent chromatin accessibility to regulation of CD8 T cell effector responses |
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| Relations |
| BioSample |
SAMN40694197 |
| SRA |
SRX24107987 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8180716_AKOVIM3_macs2_narrow_peaks.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSM8180716_AKOVIM3_macs2_narrow_treat_pileup.bw |
310.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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