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GSE213469

GSE GEO
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Open chromatin regions at the single cell level of CD8+ T cells from the spleens of LCMV-Armstrong or LCMV-Clone 13 infected mice

Organism: Mus musculus
Platform: GPL24247
Samples: 2
Experiment Types:
Genome binding/occupancy profiling by high throughput sequencing
Submitted: Sep 15 2022
Last Updated: Apr 05 2023
Status: Public on Jan 04 2023
Contact: Gene,W,Yeo (University of California, San Diego)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA880897

Summary

The profiles of open chromatin regions of CD8+ T cells from LCMV-Armstrong and LCMV-Clone 13 infected mice are known to be distinct from one another. We used Assay for Transposase-Accessible Chromatin using sequencing at the single cell level (scATAC-seq) to analyze these differences in splenic CD8+ T cells of these two infection conditions at Division 1 post-infection.

Overall Design

Adoptively transferred CD8+ P14 T cells from the spleen of C57BL/6 mice were isolated by Fluorescence-activated cell sorting (FACS) at day 2 post-infection according to the presence of CD45.1 congenic marker and CFSE signal to isolate cells undergoing their 1st division and analyzed using scATAC-seq.

Analysis (2 steps)

View Data Processing
Processing steps for GSE213469
  1. Alignment, cell barcode processing, umis processing, abundance measurements: Cellranger ATAC (version 1.2.0)
  2. QC, cell filtering, dimension reduction: Signac (version 1.5.0)

Supplementary Files (1)

GSE213469_filtered_peak_bc_matrix.h5 Download
GEO Samples (2)
GSM6586833 GSM6586834

Dataset Citations (1)

Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection.
PMID 36716323 · 2023 · PLoS biology
Lauren K Quezada, Wenhao Jin, Yi Chia Liu, Eleanor S Kim, Zhaoren He, Cynthia S Indralingam, Tiffani Tysl, Lara Labarta-Bajo, Ellen J Wehrens, Yeara Jo, Katelynn R Kazane, Christopher Hattori, Elina I Zuniga, Gene W Yeo, John T Chang

SRA Experiments (2) and Runs (8)

Total: 33040 MB
SRX17596223 SRP397493 ATAC-seq PAIRED
GSM6586833: Division 1, Armstrong, Spleen; Mus musculus; ATAC-seq
Sample: SRS15133016
BioProject: PRJNA880897
BioSample: SAMN30875388
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cells
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (4)
Run Spots Bases Size (MB) Files Link
SRR21594573 58093331 13129092806 4221.08 Div1_Arm_Spl_1_S17_L001_R1_001.fastq.gz, Div1_Arm_Spl_1_S17_L001_R2_0… SRA
SRR21594574 67223937 15192609762 4879.84 Div1_Arm_Spl_2_S18_L001_R1_001.fastq.gz, Div1_Arm_Spl_2_S18_L001_R2_0… SRA
SRR21594575 21807665 4928532290 1572.08 Div1_Arm_Spl_3_S19_L001_R1_001.fastq.gz, Div1_Arm_Spl_3_S19_L001_R2_0… SRA
SRR21594576 55965017 12648093842 4021.18 Div1_Arm_Spl_4_S20_L001_R1_001.fastq.gz, Div1_Arm_Spl_4_S20_L001_R2_0… SRA
SRX17596224 SRP397493 ATAC-seq PAIRED
GSM6586834: Division 1, Clone13, Spleen; Mus musculus; ATAC-seq
Sample: SRS15133017
BioProject: PRJNA880897
BioSample: SAMN30875387
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cells
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (4)
Run Spots Bases Size (MB) Files Link
SRR21594569 61847650 13977568900 4489.97 Div1_Cl13_Spl_1_S21_L001_R1_001.fastq.gz, Div1_Cl13_Spl_1_S21_L001_R2… SRA
SRR21594570 58558765 13234280890 4253.09 Div1_Cl13_Spl_2_S22_L001_R1_001.fastq.gz, Div1_Cl13_Spl_2_S22_L001_R2… SRA
SRR21594571 60674684 13712478584 4395.49 Div1_Cl13_Spl_3_S23_L001_R1_001.fastq.gz, Div1_Cl13_Spl_3_S23_L001_R2… SRA
SRR21594572 71642530 16191211780 5207.71 Div1_Cl13_Spl_4_S24_L001_R1_001.fastq.gz, Div1_Cl13_Spl_4_S24_L001_R2… SRA

Linked Publications (2)

Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection.
PLoS biology · 2023
Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection.
PLoS biology · 2023

Data Files (8)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— Div1_Arm_Spl_1_S17_L001_R1_001.fastq.gz ATAC-seq 4.1 GB link
— Div1_Arm_Spl_2_S18_L001_R1_001.fastq.gz ATAC-seq 4.8 GB link
— Div1_Arm_Spl_3_S19_L001_R1_001.fastq.gz ATAC-seq 1.5 GB link
— Div1_Arm_Spl_4_S20_L001_R1_001.fastq.gz ATAC-seq 3.9 GB link
— Div1_Cl13_Spl_1_S21_L001_R1_001.fastq.gz ATAC-seq 4.4 GB link
— Div1_Cl13_Spl_2_S22_L001_R1_001.fastq.gz ATAC-seq 4.2 GB link
— Div1_Cl13_Spl_3_S23_L001_R1_001.fastq.gz ATAC-seq 4.3 GB link
— Div1_Cl13_Spl_4_S24_L001_R1_001.fastq.gz ATAC-seq 5.1 GB link