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GSE213470

GSE GEO
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Gene expression profiles 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: GPL19057
Samples: 16
Experiment Types:
Expression 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/PRJNA880896

Summary

The transcriptomes of CD8+ T cells from LCMV-Armstrong and LCMV-Clone 13 infected mice are known to be distinct from one another. We used single cell RNA sequencing (scRNA-seq) to analyze the transcriptomic diversity of splenic CD8+ T cells in these two infection conditions at various timepoints after infection.

Overall Design

Adoptively transferred CD8+ P14 T cells from the spleen of C57BL/6 mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence of CD45.1 congenic signal and analyzed using scRNA-seq.

Analysis (2 steps)

View Data Processing
Processing steps for GSE213470
  1. Alignment, cell barcode processing, umis processing, abundance measurements: cellranger count (version 2.1.1)
  2. Cells and genes filtering, dimension reduction: Scanpy (version 1.7.2)

Supplementary Files (2)

GSE213470_Metadata4Wenhao_Cl13.csv.gz Download
GSE213470_UMI4Wenhao_Cl13_full_table.csv.gz Download
GEO Samples (16)
GSM6586835 GSM6586836 GSM6586837 GSM6586838 GSM6586839 GSM6586840 GSM6586841 GSM6586842 GSM6586843 GSM6586844 GSM6586845 GSM6586846 GSM6586847 GSM6586848 GSM6586849 GSM6586850

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 (16) and Runs (16)

Total: 63037 MB
SRX17596344 SRP397498 RNA-Seq PAIRED
GSM6586839: Day 6, Armstrong; Mus musculus; RNA-Seq
Sample: SRS15133137
BioProject: PRJNA880896
BioSample: SAMN30875476
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594711 30526595 3785297780 1770.44 LQ_10X_D6_Arm_R1.fastq.gz, LQ_10X_D6_Arm_R2.fastq.gz, SRR21594711, SR… SRA
SRX17596345 SRP397498 RNA-Seq PAIRED
GSM6586840: Day 7, Armstrong; Mus musculus; RNA-Seq
Sample: SRS15133138
BioProject: PRJNA880896
BioSample: SAMN30875475
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594710 45380112 5627133888 2564.94 LQ_10X_D7_Arm_R1.fastq.gz, LQ_10X_D7_Arm_R2.fastq.gz, SRR21594710, SR… SRA
SRX17596346 SRP397498 RNA-Seq PAIRED
GSM6586841: Day 8, Armstrong; Mus musculus; RNA-Seq
Sample: SRS15133139
BioProject: PRJNA880896
BioSample: SAMN30875474
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594709 42743566 5300202184 2427.49 LQ_10X_D8_Arm_R1.fastq.gz, LQ_10X_D8_Arm_R2.fastq.gz, SRR21594709, SR… SRA
SRX17596347 SRP397498 RNA-Seq PAIRED
GSM6586842: Day 22, Armstrong; Mus musculus; RNA-Seq
Sample: SRS15133140
BioProject: PRJNA880896
BioSample: SAMN30875473
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594708 58388837 7240215788 3301.35 LQ_10X_D22_Arm_R1.fastq.gz, LQ_10X_D22_Arm_R2.fastq.gz, SRR21594708, … SRA
SRX17596348 SRP397498 RNA-Seq PAIRED
GSM6586843: Day 60, Armstrong; Mus musculus; RNA-Seq
Sample: SRS15133141
BioProject: PRJNA880896
BioSample: SAMN30875472
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594707 105920064 13134087936 6348.14 LQ_10X_D60_Arm_R1.fastq.gz, LQ_10X_D60_Arm_R2.fastq.gz, SRR21594707, … SRA
SRX17596349 SRP397498 RNA-Seq PAIRED
GSM6586844: Division 1, Clone 13; Mus musculus; RNA-Seq
Sample: SRS15133142
BioProject: PRJNA880896
BioSample: SAMN30875471
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594706 78477995 9731271380 4654.92 LQ_10X_Div_1_Cl13_R1.fastq.gz, LQ_10X_Div_1_Cl13_R2.fastq.gz, SRR2159… SRA
SRX17596350 SRP397498 RNA-Seq PAIRED
GSM6586845: Day 3, Clone13; Mus musculus; RNA-Seq
Sample: SRS15133143
BioProject: PRJNA880896
BioSample: SAMN30875470
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594705 50470400 6258329600 2962.13 LQ_10X_D3_Cl13_R1.fastq.gz, LQ_10X_D3_Cl13_R2.fastq.gz, SRR21594705, … SRA
SRX17596351 SRP397498 RNA-Seq PAIRED
GSM6586846: Day 5, Clone14; Mus musculus; RNA-Seq
Sample: SRS15133144
BioProject: PRJNA880896
BioSample: SAMN30875469
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594704 46842071 5808416804 2670.09 LQ_D5_Cl13_Re-Do_R1.fastq.gz, LQ_D5_Cl13_Re-Do_R2.fastq.gz, SRR215947… SRA
SRX17596352 SRP397498 RNA-Seq PAIRED
GSM6586847: Day 8, Clone15; Mus musculus; RNA-Seq
Sample: SRS15133145
BioProject: PRJNA880896
BioSample: SAMN30875468
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594703 112010131 13889256244 6673.69 LQ_10X_D8_Cl13_R1.fastq.gz, LQ_10X_D8_Cl13_R2.fastq.gz, SRR21594703, … SRA
SRX17596353 SRP397498 RNA-Seq PAIRED
GSM6586848: Day 22, Clone16; Mus musculus; RNA-Seq
Sample: SRS15133146
BioProject: PRJNA880896
BioSample: SAMN30875467
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594702 37664108 4670349392 2164.98 LQ_D22_Cl13_Re-do_R1.fastq.gz, LQ_D22_Cl13_Re-do_R2.fastq.gz, SRR2159… SRA
SRX17596354 SRP397498 RNA-Seq PAIRED
GSM6586849: Day 34, Clone17; Mus musculus; RNA-Seq
Sample: SRS15133147
BioProject: PRJNA880896
BioSample: SAMN30875466
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594701 33963255 4211443620 1970.39 LQ_D34_Cl13_Re-do_R1.fastq.gz, LQ_D34_Cl13_Re-do_R2.fastq.gz, SRR2159… SRA
SRX17596355 SRP397498 RNA-Seq PAIRED
GSM6586850: Day 60, Clone18; Mus musculus; RNA-Seq
Sample: SRS15133148
BioProject: PRJNA880896
BioSample: SAMN30875465
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594700 89413453 11087268172 5224.41 LQ_10X_D60_Cl13_R1.fastq.gz, LQ_10X_D60_Cl13_R2.fastq.gz, SRR21594700… SRA
SRX17596356 SRP397498 RNA-Seq PAIRED
GSM6586835: Naïve state; Mus musculus; RNA-Seq
Sample: SRS15133149
BioProject: PRJNA880896
BioSample: SAMN30875480
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594699 97336823 12069766052 5778.26 LQ_10X_Naive_R1.fastq.gz, LQ_10X_Naive_R2.fastq.gz, SRR21594699, SRR2… SRA
SRX17596357 SRP397498 RNA-Seq PAIRED
GSM6586836: Division 1, Armstrong; Mus musculus; RNA-Seq
Sample: SRS15133150
BioProject: PRJNA880896
BioSample: SAMN30875479
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594698 78505430 9734673320 4590.03 LQ_10X_Div_1_Arm_R1.fastq.gz, LQ_10X_Div_1_Arm_R2.fastq.gz, SRR215946… SRA
SRX17596358 SRP397498 RNA-Seq PAIRED
GSM6586837: Day 3, Armstrong; Mus musculus; RNA-Seq
Sample: SRS15133151
BioProject: PRJNA880896
BioSample: SAMN30875478
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594697 82949617 10285752508 4865.26 LQ_10X_D3_Arm_final_R1.fastq.gz, LQ_10X_D3_Arm_final_R2.fastq.gz, SRR… SRA
SRX17596359 SRP397498 RNA-Seq PAIRED
GSM6586838: Day 5, Armstrong; Mus musculus; RNA-Seq
Sample: SRS15133152
BioProject: PRJNA880896
BioSample: SAMN30875477
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cell
tissue: Spleen
strain: C57BL/6
age: 7-10 weeks old
Original files (1)
Spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594696 87452172 10844069328 5070.6 LQ_10X_D5_Arm_R1.fastq.gz, LQ_10X_D5_Arm_R2.fastq.gz, SRR21594696, SR… SRA

Linked Publications (1)

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

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.

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

Data Files (32)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— LQ_10X_D22_Arm_R1.fastq.gz RNA-Seq 3.2 GB link
— LQ_10X_D3_Arm_final_R1.fastq.gz RNA-Seq 4.8 GB link
— LQ_10X_D3_Cl13_R1.fastq.gz RNA-Seq 2.9 GB link
— LQ_10X_D5_Arm_R1.fastq.gz RNA-Seq 5.0 GB link
— LQ_10X_D60_Arm_R1.fastq.gz RNA-Seq 6.2 GB link
— LQ_10X_D60_Cl13_R1.fastq.gz RNA-Seq 5.1 GB link
— LQ_10X_D6_Arm_R1.fastq.gz RNA-Seq 1.7 GB link
— LQ_10X_D7_Arm_R1.fastq.gz RNA-Seq 2.5 GB link
— LQ_10X_D8_Arm_R1.fastq.gz RNA-Seq 2.4 GB link
— LQ_10X_D8_Cl13_R1.fastq.gz RNA-Seq 6.5 GB link
— LQ_10X_Div_1_Arm_R1.fastq.gz RNA-Seq 4.5 GB link
— LQ_10X_Div_1_Cl13_R1.fastq.gz RNA-Seq 4.5 GB link
— LQ_10X_Naive_R1.fastq.gz RNA-Seq 5.6 GB link
— LQ_D22_Cl13_Re-do_R1.fastq.gz RNA-Seq 2.1 GB link
— LQ_D34_Cl13_Re-do_R1.fastq.gz RNA-Seq 1.9 GB link
— LQ_D5_Cl13_Re-Do_R1.fastq.gz RNA-Seq 2.6 GB link
— SRR21594696_GSM6586838 RNA-Seq 5.0 GB link
— SRR21594697_GSM6586837 RNA-Seq 4.8 GB link
— SRR21594698_GSM6586836 RNA-Seq 4.5 GB link
— SRR21594699_GSM6586835 RNA-Seq 5.6 GB link
— SRR21594700_GSM6586850 RNA-Seq 5.1 GB link
— SRR21594701_GSM6586849 RNA-Seq 1.9 GB link
— SRR21594702_GSM6586848 RNA-Seq 2.1 GB link
— SRR21594703_GSM6586847 RNA-Seq 6.5 GB link
— SRR21594704_GSM6586846 RNA-Seq 2.6 GB link
— SRR21594705_GSM6586845 RNA-Seq 2.9 GB link
— SRR21594706_GSM6586844 RNA-Seq 4.5 GB link
— SRR21594707_GSM6586843 RNA-Seq 6.2 GB link
— SRR21594708_GSM6586842 RNA-Seq 3.2 GB link
— SRR21594709_GSM6586841 RNA-Seq 2.4 GB link
— SRR21594710_GSM6586840 RNA-Seq 2.5 GB link
— SRR21594711_GSM6586839 RNA-Seq 1.7 GB link