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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 (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 (16)

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