← All datasets

GSE157072

GSE GEO
View on GEO Export SRA CSV

RNA-Seq of CD8+ T cell subsets during LCMV infection III

Organism: Mus musculus
Platform: GPL17021
Samples: 16
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Aug 28 2020
Last Updated: Dec 09 2020
Status: Public on Aug 29 2020
Contact: Ananda,,Goldrath (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA660017 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP279222

Summary

Memory CD8 T lymphocytes are a long-lived population of immune cells that provide formidable protection against infections and malignancy, and are thus often central to vaccine and cancer immunotherapy efficacy. Here we refine the identity, developmental relationships, and functional roles of memory CD8 T cells through delineation of a descrete population that confers robust protection against reinfection and exhibits an unexpected molecular program bearing typically divergent characteristics of short-lived effector cells and long-lived memory T cells. Mass-cytometry and single-cell RNA sequencing analyses revealed an analogous population of cells in humans. These findings hold broad implications for both informing immunotherapy treatments and predicting their efficacy.

Overall Design

16 samples, 2 replicates, Day 55 LCMV infection CD8+ T cell subsets, Day 7 LCMV infection CD8+ effector T cells, Naive CD8+ T cells This series includes samples re-analyzed from GSE107281 and GSE147080. These re-analyzed samples have been included here so that all raw data for this study is available from a single SRP.

Analysis (3 steps)

View Data Processing
Processing steps for GSE157072
  1. Tophat
  2. HT-Seq Count
  3. DESeq from BioConductor

Supplementary Files (1)

GSE157072_Processed_D55_LCMV_RNAseq.txt.gz Download
GEO Samples (16)
GSM4751934 GSM4751935 GSM4751936 GSM4751937 GSM4751938 GSM4751939 GSM4751940 GSM4751941 GSM4751942 GSM4751943 GSM4751944 GSM4751945 GSM4751946 GSM4751947 GSM4751948 GSM4751949

Dataset Citations (1)

PubMed citation (PMID 32978300)

SRA Experiments (16) and Runs (16)

Total: 3466 MB
SRX9030343 SRP279222 RNA-Seq PAIRED
GSM4751934: IEL.Trm.1; Mus musculus; RNA-Seq
Sample: SRS7281624
BioProject: PRJNA660017
BioSample: SAMN15932337
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D55 CD103hiCD62Lhi IEL Trm P14
strain: C57BL/6
age: 6-16 Weeks
tissue: Small intestine IEL
cell type: CD8+ T cells
Original files (1)
D55 CD103hiCD62Lhi IEL Trm P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540684 15105542 755277100 270.69 000008565169_G09.R1.fastq, 000008565169_G09.R2.fastq, SRR12540684, SR… SRA
SRX9030344 SRP279222 RNA-Seq PAIRED
GSM4751935: IEL.Trm.2; Mus musculus; RNA-Seq
Sample: SRS7281625
BioProject: PRJNA660017
BioSample: SAMN15932336
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D55 CD103hiCD62Lhi IEL Trm P14
strain: C57BL/6
age: 6-16 Weeks
tissue: Small intestine IEL
cell type: CD8+ T cells
Original files (1)
D55 CD103hiCD62Lhi IEL Trm P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540685 13009938 650496900 234.05 000008565169_H09.R1.fastq, 000008565169_H09.R2.fastq, SRR12540685, SR… SRA
SRX9030345 SRP279222 RNA-Seq PAIRED
GSM4751936: Sp.ttem.1; Mus musculus; RNA-Seq
Sample: SRS7281626
BioProject: PRJNA660017
BioSample: SAMN15932335
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D55 CD127loCD62Llo terminal Tem P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D55 CD127loCD62Llo terminal Tem P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540686 13835059 691752950 248.3 000008565169_A10.R1.fastq, 000008565169_A10.R2.fastq, SRR12540686, SR… SRA
SRX9030346 SRP279222 RNA-Seq PAIRED
GSM4751937: SP.ttem.2; Mus musculus; RNA-Seq
Sample: SRS7281627
BioProject: PRJNA660017
BioSample: SAMN15932334
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D55 CD127loCD62Llo terminal Tem P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D55 CD127loCD62Llo terminal Tem P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540687 13987040 699352000 251.02 000008565169_B10.R1.fastq, 000008565169_B10.R2.fastq, SRR12540687, SR… SRA
SRX9030347 SRP279222 RNA-Seq PAIRED
GSM4751938: Sp.Conv.TEM.1; Mus musculus; RNA-Seq
Sample: SRS7281628
BioProject: PRJNA660017
BioSample: SAMN15932333
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D55 CD62Llo Conventional Tem P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D55 CD62Llo Conventional Tem P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540688 10655721 532786050 192.67 SRR12540688.lite, SRR12540688, 000008565169_C10.R2.fastq, 00000856516… SRA
SRX9030348 SRP279222 RNA-Seq PAIRED
GSM4751939: Sp.Conv.TEM.2; Mus musculus; RNA-Seq
Sample: SRS7281629
BioProject: PRJNA660017
BioSample: SAMN15932332
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D55 CD62Llo Conventional Tem P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D55 CD62Llo Conventional Tem P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540689 13228964 661448200 236.59 000008565169_D10.R1.fastq, 000008565169_D10.R2.fastq, SRR12540689, SR… SRA
SRX9030349 SRP279222 RNA-Seq PAIRED
GSM4751940: Sp.TCM.1; Mus musculus; RNA-Seq
Sample: SRS7281630
BioProject: PRJNA660017
BioSample: SAMN15932331
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D55 CD127hiCD62Lhi Tcm P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D55 CD127hiCD62Lhi Tcm P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540690 12739824 636991200 230.49 000008565169_G10.R1.fastq, 000008565169_G10.R2.fastq, SRR12540690, SR… SRA
SRX9030350 SRP279222 RNA-Seq PAIRED
GSM4751941: Sp.TCM.2; Mus musculus; RNA-Seq
Sample: SRS7281631
BioProject: PRJNA660017
BioSample: SAMN15932330
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D55 CD127hiCD62Lhi Tcm P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D55 CD127hiCD62Lhi Tcm P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540691 12594399 629719950 225.85 000008565169_H10.R1.fastq, 000008565169_H10.R2.fastq, SRR12540691, SR… SRA
SRX9030351 SRP279222 RNA-Seq PAIRED
GSM4751942: Sp.TEM.1; Mus musculus; RNA-Seq
Sample: SRS7281632
BioProject: PRJNA660017
BioSample: SAMN15932329
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D55 CD127hiCD62Llo Tem P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D55 CD127hiCD62Llo Tem P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540692 10860301 543015050 200.77 000008565169_E10.R1.fastq.gz, 000008565169_E10.R2.fastq.gz, SRR125406… SRA
SRX9030352 SRP279222 RNA-Seq PAIRED
GSM4751943: Sp.TEM.2; Mus musculus; RNA-Seq
Sample: SRS7281633
BioProject: PRJNA660017
BioSample: SAMN15932328
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D55 CD127hiCD62Llo Tem P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D55 CD127hiCD62Llo Tem P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540693 11967481 598374050 214.93 SRR12540693.lite, SRR12540693, 000008565169_F10.R2.fastq.gz, 00000856… SRA
SRX9030353 SRP279222 RNA-Seq PAIRED
GSM4751944: T8.MP.LCMV.D7.Sp1; Mus musculus; RNA-Seq
Sample: SRS7281634
BioProject: PRJNA660017
BioSample: SAMN15932347
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D7 CD127hi KLRG1lo MP P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D7 CD127hi KLRG1lo MP P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540694 11233047 561652350 234.23 SSF1856_F04.R1.fastq, SSF1856_F04.R2.fastq, SRR12540694, SRR12540694.… SRA
SRX9030354 SRP279222 RNA-Seq PAIRED
GSM4751945: T8.MP.LCMV.D7.Sp2; Mus musculus; RNA-Seq
Sample: SRS7281635
BioProject: PRJNA660017
BioSample: SAMN15932346
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D7 CD127hi KLRG1lo MP P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D7 CD127hi KLRG1lo MP P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540695 10585647 529282350 213.89 SRR12540695.lite, SRR12540695, SSF1857_F04.R2.fastq, SSF1857_F04.R1.f… SRA
SRX9030355 SRP279222 RNA-Seq PAIRED
GSM4751946: T8.TE.LCMV.D7.Sp1; Mus musculus; RNA-Seq
Sample: SRS7281636
BioProject: PRJNA660017
BioSample: SAMN15932345
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D7 CD127lo KLRG1hi TE P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D7 CD127lo KLRG1hi TE P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540696 12195012 609750600 255.32 SSF1856_E04.R1.fastq, SSF1856_E04.R2.fastq, SRR12540696, SRR12540696.… SRA
SRX9030356 SRP279222 RNA-Seq PAIRED
GSM4751947: T8.TE.LCMV.D7.Sp2; Mus musculus; RNA-Seq
Sample: SRS7281637
BioProject: PRJNA660017
BioSample: SAMN15932344
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: D7 CD127lo KLRG1hi TE P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
D7 CD127lo KLRG1hi TE P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540697 8307214 415360700 169.13 SSF1857_E04.R1.fastq, SSF1857_E04.R2.fastq, SRR12540697, SRR12540697.… SRA
SRX9030357 SRP279222 RNA-Seq PAIRED
GSM4751948: T8.TN.P14.Sp1; Mus musculus; RNA-Seq
Sample: SRS7281638
BioProject: PRJNA660017
BioSample: SAMN15932343
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: CD62Lhi CD44lo P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
CD62Lhi CD44lo P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540698 8119022 405951100 172.75 SSF1856_D04.R1.fastq, SSF1856_D04.R2.fastq, SRR12540698, SRR12540698.… SRA
SRX9030358 SRP279222 RNA-Seq PAIRED
GSM4751949: T8.TN.P14.Sp2; Mus musculus; RNA-Seq
Sample: SRS7281639
BioProject: PRJNA660017
BioSample: SAMN15932342
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: CD62Lhi CD44lo P14
strain: C57BL/6
age: 6-16 Weeks
tissue: spleen
cell type: CD8+ T cells
Original files (1)
CD62Lhi CD44lo P14
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR12540699 5583440 279172000 115.05 SSF1857_D04.R1.fastq, SSF1857_D04.R2.fastq, SRR12540699, SRR12540699.… SRA

Linked Publications (1)

The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression.
The Journal of experimental medicine · 2022

Data Files (16)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— 000008565169_A10.R1.fastq RNA-Seq 248.3 MB link
— 000008565169_B10.R1.fastq RNA-Seq 251.0 MB link
— 000008565169_D10.R1.fastq RNA-Seq 236.6 MB link
— 000008565169_E10.R1.fastq.gz RNA-Seq 200.8 MB link
— 000008565169_G09.R1.fastq RNA-Seq 270.7 MB link
— 000008565169_G10.R1.fastq RNA-Seq 230.5 MB link
— 000008565169_H09.R1.fastq RNA-Seq 234.0 MB link
— 000008565169_H10.R1.fastq RNA-Seq 225.8 MB link
— SRR12540688.lite RNA-Seq 192.7 MB link
— SRR12540693.lite RNA-Seq 214.9 MB link
— SRR12540695.lite RNA-Seq 213.9 MB link
— SSF1856_D04.R1.fastq RNA-Seq 172.8 MB link
— SSF1856_E04.R1.fastq RNA-Seq 255.3 MB link
— SSF1856_F04.R1.fastq RNA-Seq 234.2 MB link
— SSF1857_D04.R1.fastq RNA-Seq 115.0 MB link
— SSF1857_E04.R1.fastq RNA-Seq 169.1 MB link