GSE213469
GSE GEOOpen 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
- Alignment, cell barcode processing, umis processing, abundance measurements: Cellranger ATAC (version 1.2.0)
- QC, cell filtering, dimension reduction: Signac (version 1.5.0)
Supplementary Files (1)
GSE213469_filtered_peak_bc_matrix.h5
Download
GEO Samples (2)
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 MBGSM6586833: 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 |
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 (1)
Potentially Related Publications (1)
This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.
Data Files (16)
| 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 | |||
| — | SRR21594569_GSM6586834 | ATAC-seq | 4.4 GB | link | |||
| — | SRR21594570_GSM6586834 | ATAC-seq | 4.2 GB | link | |||
| — | SRR21594571_GSM6586834 | ATAC-seq | 4.3 GB | link | |||
| — | SRR21594572_GSM6586834 | ATAC-seq | 5.1 GB | link | |||
| — | SRR21594573_GSM6586833 | ATAC-seq | 4.1 GB | link | |||
| — | SRR21594574_GSM6586833 | ATAC-seq | 4.8 GB | link | |||
| — | SRR21594575_GSM6586833 | ATAC-seq | 1.5 GB | link | |||
| — | SRR21594576_GSM6586833 | ATAC-seq | 3.9 GB | link |