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| Status |
Public on Jul 25, 2023 |
| Title |
Day9 Tcf7-YFP high, sorted Tcf7-YFP low at Day3, 3 (ATAC-seq) |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: CD8+ T cell
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sorted cells were centrifuged and frozen in ATAC freezing buffer and stored at -80°C. For processing, cells were thawed, centrifuged, washed with PBS and lysed. Nuclei were then subjected to tagementation and purification.
Purfied tagmented DNA was PCR amplifed using Illumina indexed primers and NEBNext High-Fidelity 2X PCR Master Mix. Pooled libraries were sequenced on a NextSeq 500 High150 cycle kit with paired end sequencing (read 1: 74 cycles, read 2: 74 cycles, index 1: 10 cycles, index 2: 10 cycles)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw fastq files were processed and aligned to the mm10 mouse genome using the PEPATAC (v0.10.3) pipeline, which uses bowtie2 for alignment. Unmapped, unpaired, and mitochondrial reads were removed.
Following alignment, peak calling, merging across all samples, and annotation was performed using HOMER (v4.10). The peaks.txt processed data files represent the individual sample peak counts prior to identifying consensus peaks. The HOMER commands used to generate peak counts from bam files were: makeTagDirectory, findPeaks (parameters: -style factor -o auto), mergePeaks (parameters: -d 150), annotatePeaks.pl (parameters: mm10 -size "given" -raw -d)
Differentially accessible regions were identified using DESeq2.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: The peaks.txt file for each sample was generated from HOMER findPeaks and contains columns with peakID, peak information, and normalized counts.
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| Submission date |
Jul 20, 2023 |
| Last update date |
Jul 25, 2023 |
| Contact name |
Kathleen Abadie |
| E-mail(s) |
abadiek@uw.edu
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| Organization name |
University of Washington
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| Department |
Bioengineering
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| Lab |
Kueh Lab
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| Street address |
3720 15th Ave NE
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| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE237827 |
Flexible and scalable control of T cell memory by a reversible epigenetic switch (ATAC-seq) |
| GSE237830 |
Flexible and scalable control of T cell memory by a reversible epigenetic switch |
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| Relations |
| BioSample |
SAMN36656109 |
| SRA |
SRX21106733 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7655050_O3_M3_D9_S11_smooth.bw |
2.2 Gb |
(ftp)(http) |
BW |
| GSM7655050_S11_peaks.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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