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GSE213467

GSE GEO
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Areas of H3K27 tri-methylation in CD8+ T cells from the spleens of LCMV-Armstrong or LCMV-Clone 13 infected mice

Organism: Mus musculus
Platform: GPL24247
Samples: 6
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/PRJNA880890

Summary

The profiles of H3K27 tri-methylation in CD8+ T cells from LCMV-Armstrong and LCMV-Clone 13 infected mice are known to be distinct from one another. We used CUT&RUN (Cleavage Under Targets and Release Using Nuclease) to analyze these differences in splenic CD8+ T cells of these two infection conditions.

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 7 post-infection according to the presence of CD45.1 congenic marker signal and analyzed using CUT&RUN.

Analysis (11 steps)

View Data Processing
Processing steps for GSE213467
  1. Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
  2. Reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.38, discarding reads left with < 25 bp
  3. Reads were aligned to the mouse genome (mm10) using Bowtie version 1.1.2.
  4. Parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
  5. Reads were aligned to the yeast genome (sacCer3) using Bowtie version 1.1.2.
  6. Parameters: --local --very-sensitive-local --no-overlap --no-dovetail --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 70
  7. Spike-in normalization.
  8. The genomic coverage were then normalized by applying the scaling factor that is calculated from the number of mapped reads to mouse genome and yeast genome
Showing first 8 steps.

Supplementary Files (1)

GSE213467_RAW.tar Download
GEO Samples (6)
GSM6586821 GSM6586822 GSM6586823 GSM6586824 GSM6586825 GSM6586826

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 (6) and Runs (6)

Total: 23654 MB
SRX17596194 SRP397491 ChIP-Seq PAIRED
GSM6586821: H3K27me3, Armstrong; Mus musculus; ChIP-Seq
Sample: SRS15133009
BioProject: PRJNA880890
BioSample: SAMN30875303
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: spleen
tissue: spleen
cell type: CD8 T Cell
chip antibody: H3K27me3 (CST, #9733)
Original files (1)
spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594545 105684042 21348176484 6714.41 4-H3K27me3_A2_S39_L002_R1_001.fastq.gz, 4-H3K27me3_A2_S39_L002_R2_001… SRA
SRX17596195 SRP397491 ChIP-Seq PAIRED
GSM6586822: H3K27me3, Clone13; Mus musculus; ChIP-Seq
Sample: SRS15133010
BioProject: PRJNA880890
BioSample: SAMN30875302
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: spleen
tissue: spleen
cell type: CD8 T Cell
chip antibody: H3K27me3 (CST, #9733)
Original files (1)
spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594544 32216646 6507762492 2031.3 10-H3K27me3_C2_S45_L002_R1_001.fastq.gz, 10-H3K27me3_C2_S45_L002_R2_0… SRA
SRX17596196 SRP397491 ChIP-Seq PAIRED
GSM6586823: H3K4me3, Armstrong; Mus musculus; ChIP-Seq
Sample: SRS15133011
BioProject: PRJNA880890
BioSample: SAMN30875301
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: spleen
tissue: spleen
cell type: CD8 T Cell
chip antibody: H3K4me3 (CST, #9751)
Original files (1)
spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594543 47144031 9523094262 2966.14 2-H3K4me3_A2_S37_L002_R1_001.fastq.gz, 2-H3K4me3_A2_S37_L002_R2_001.f… SRA
SRX17596197 SRP397491 ChIP-Seq PAIRED
GSM6586824: H3K4me3, Clone13; Mus musculus; ChIP-Seq
Sample: SRS15133012
BioProject: PRJNA880890
BioSample: SAMN30875300
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: spleen
tissue: spleen
cell type: CD8 T Cell
chip antibody: H3K4me3 (CST, #9751)
Original files (1)
spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594542 38608336 7798883872 2422.55 8-H3K4me3_C2_S43_L002_R1_001.fastq.gz, 8-H3K4me3_C2_S43_L002_R2_001.f… SRA
SRX17596198 SRP397491 ChIP-Seq PAIRED
GSM6586825: IgG, Armstrong; Mus musculus; ChIP-Seq
Sample: SRS15133013
BioProject: PRJNA880890
BioSample: SAMN30875299
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: spleen
tissue: spleen
cell type: CD8 T Cell
chip antibody: Rabbit IgG XP (CST, #66362)
Original files (1)
spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594541 87479096 17670777392 5534.37 6-IgG_A2_S41_L002_R1_001.fastq.gz, 6-IgG_A2_S41_L002_R2_001.fastq.gz,… SRA
SRX17596199 SRP397491 ChIP-Seq PAIRED
GSM6586826: IgG, Clone13; Mus musculus; ChIP-Seq
Sample: SRS15133014
BioProject: PRJNA880890
BioSample: SAMN30875298
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: spleen
tissue: spleen
cell type: CD8 T Cell
chip antibody: Rabbit IgG XP (CST, #66362)
Original files (1)
spleen
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR21594540 63212616 12768948432 3985.31 12-IgG_C2_S47_L002_R1_001.fastq.gz, 12-IgG_C2_S47_L002_R2_001.fastq.g… 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 (6)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— 10-H3K27me3_C2_S45_L002_R1_001.fastq.gz ChIP-Seq 2.0 GB link
— 12-IgG_C2_S47_L002_R1_001.fastq.gz ChIP-Seq 3.9 GB link
— 2-H3K4me3_A2_S37_L002_R1_001.fastq.gz ChIP-Seq 2.9 GB link
— 4-H3K27me3_A2_S39_L002_R1_001.fastq.gz ChIP-Seq 6.6 GB link
— 6-IgG_A2_S41_L002_R1_001.fastq.gz ChIP-Seq 5.4 GB link
— 8-H3K4me3_C2_S43_L002_R1_001.fastq.gz ChIP-Seq 2.4 GB link