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GSE203086

GSE GEO
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The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression (scRNA-Seq)

Organism: Mus musculus
Platform: GPL21103
Samples: 4
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: May 16 2022
Last Updated: Aug 19 2022
Status: Public on May 18 2022
Contact: John,,Chang (UC San Diego)

Relations

SubSeries of: GSE203092 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA838564

Summary

The long noncoding RNA Malat1 impacts the differentiation of effector and memory CD8+ T cell subsets by virtue of preferential epigenetic repression of memory-associated genes in terminal effector cells through an interaction with Ezh2

Overall Design

Malat1 Knockdown and Nontarget P14 CD8+ T cells were sorted 7 days after LCMV infection

Analysis (10 steps)

View Data Processing
Processing steps for GSE203086
  1. Reads from scRNA-seq were aligned to mm10 using the 10x Genomics Cell Ranger software (v 2.1.0).
  2. Reads were collapsed into unique molecular identifier counts.
  3. All samples had >2000 cells detected with >1000 genes per cells with >70% of the coding genome covered.
  4. Genes that were not expressed in at least 5% of all cells were excluded.
  5. As previously described (Boland et al., 2020), replicates of single cell libraries were normalized removing batch effects using RUVnormalize (v1.15.0).
  6. The raw UMI matrix was scaled and input to the naiveRandRUV function with parameters coeff=1e-3 and k=10.
  7. Fifty negative control genes were taken from a list of housekeeping genes (Eisenberg and Levanon, 2013) with least variability in all datasets.
  8. Seurat (v3.0.1) functions were used to calculate top variable genes, principal components analysis (PCA), and tSNE with FindVariableGenes, RunPCA, and RunTSNE.
Showing first 8 steps.

Supplementary Files (1)

GSE203086_RAW.tar Download
GEO Samples (4)
GSM6153598 GSM6153599 GSM6153600 GSM6153601

Dataset Citations (1)

The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression.
PMID 35593887 · 2022 · The Journal of experimental medicine
Jad N Kanbar, Shengyun Ma, Eleanor S Kim, Nadia S Kurd, Matthew S Tsai, Tiffani Tysl, Christella E Widjaja, Abigail E Limary, Brian Yee, Zhaoren He, Yajing Hao, Xiang-Dong Fu, Gene W Yeo, Wendy J Huang, John T Chang

SRA Experiments (4) and Runs (16)

Total: 9239 MB
SRX15281819 SRP375364 RNA-Seq PAIRED
GSM6153598: Day7 Malat1 Knockdown, replicate 1, scRNAseq; Mus musculus; RNA-Seq
Sample: SRS13013219
BioProject: PRJNA838564
BioSample: SAMN28448175
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cells
tissue: Spleen
strain: C57BL/6
age: 6-8 weeks old
Original files (1)
Spleen
Runs (4)
Run Spots Bases Size (MB) Files Link
SRR19217849 9210005 1142040620 539.25 Day_7_MALAT1_1_S21_L008_R1_001.fastq.gz, Day_7_MALAT1_1_S21_L008_R2_0… SRA
SRR19217850 12328439 1528726436 726.99 Day_7_MALAT1_1_S22_L008_R1_001.fastq.gz, Day_7_MALAT1_1_S22_L008_R2_0… SRA
SRR19217851 8423749 1044544876 505.4 Day_7_MALAT1_1_S23_L008_R1_001.fastq.gz, Day_7_MALAT1_1_S23_L008_R2_0… SRA
SRR19217852 8251952 1023242048 483.99 Day_7_MALAT1_1_S24_L008_R1_001.fastq.gz, Day_7_MALAT1_1_S24_L008_R2_0… SRA
SRX15281820 SRP375364 RNA-Seq PAIRED
GSM6153599: Day7 Malat1 Knockdown, replicate 2, scRNAseq; Mus musculus; RNA-Seq
Sample: SRS13013220
BioProject: PRJNA838564
BioSample: SAMN28448174
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cells
tissue: Spleen
strain: C57BL/6
age: 6-8 weeks old
Original files (1)
Spleen
Runs (4)
Run Spots Bases Size (MB) Files Link
SRR19217845 10436947 1294181428 612.01 Day_7_MALAT1_2_S29_L008_R1_001.fastq.gz, Day_7_MALAT1_2_S29_L008_R2_0… SRA
SRR19217846 7638115 947126260 445.03 Day_7_MALAT1_2_S30_L008_R1_001.fastq.gz, Day_7_MALAT1_2_S30_L008_R2_0… SRA
SRR19217847 13502461 1674305164 793.5 Day_7_MALAT1_2_S31_L008_R1_001.fastq.gz, Day_7_MALAT1_2_S31_L008_R2_0… SRA
SRR19217848 11116083 1378394292 644.14 Day_7_MALAT1_2_S32_L008_R1_001.fastq.gz, Day_7_MALAT1_2_S32_L008_R2_0… SRA
SRX15281821 SRP375364 RNA-Seq PAIRED
GSM6153600: Day7 Nontarget, replicate 1, scRNAseq; Mus musculus; RNA-Seq
Sample: SRS13013221
BioProject: PRJNA838564
BioSample: SAMN28448173
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cells
tissue: Spleen
strain: C57BL/6
age: 6-8 weeks old
Original files (1)
Spleen
Runs (4)
Run Spots Bases Size (MB) Files Link
SRR19217841 8500603 1054074772 495.04 Day_7_Control_1_S17_L008_R1_001.fastq.gz, Day_7_Control_1_S17_L008_R2… SRA
SRR19217842 9150939 1134716436 532.64 Day_7_Control_1_S18_L008_R1_001.fastq.gz, Day_7_Control_1_S18_L008_R2… SRA
SRR19217843 13348632 1655230368 778.93 Day_7_Control_1_S19_L008_R1_001.fastq.gz, Day_7_Control_1_S19_L008_R2… SRA
SRR19217844 7593441 941586684 445.87 Day_7_Control_1_S20_L008_R1_001.fastq.gz, Day_7_Control_1_S20_L008_R2… SRA
SRX15281822 SRP375364 RNA-Seq PAIRED
GSM6153601: Day7 Nontarget, replicate 2, scRNAseq; Mus musculus; RNA-Seq
Sample: SRS13013222
BioProject: PRJNA838564
BioSample: SAMN28448172
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Spleen
cell type: CD8 T cells
tissue: Spleen
strain: C57BL/6
age: 6-8 weeks old
Original files (1)
Spleen
Runs (4)
Run Spots Bases Size (MB) Files Link
SRR19217837 11496248 1425534752 672.6 Day_7_Control_2_S25_L008_R1_001.fastq.gz, Day_7_Control_2_S25_L008_R2… SRA
SRR19217838 7375289 914535836 424.78 Day_7_Control_2_S26_L008_R1_001.fastq.gz, Day_7_Control_2_S26_L008_R2… SRA
SRR19217839 10292886 1276317864 613.2 Day_7_Control_2_S27_L008_R1_001.fastq.gz, Day_7_Control_2_S27_L008_R2… SRA
SRR19217840 8946342 1109346408 525.51 Day_7_Control_2_S28_L008_R1_001.fastq.gz, Day_7_Control_2_S28_L008_R2… 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 (33)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— Day_7_Control_1_S17_L008_R1_001.fastq.gz RNA-Seq 495.0 MB link
— Day_7_Control_1_S18_L008_R1_001.fastq.gz RNA-Seq 532.6 MB link
— Day_7_Control_1_S19_L008_R1_001.fastq.gz RNA-Seq 778.9 MB link
— Day_7_Control_1_S20_L008_R1_001.fastq.gz RNA-Seq 445.9 MB link
— Day_7_Control_2_S25_L008_R1_001.fastq.gz RNA-Seq 672.6 MB link
— Day_7_Control_2_S26_L008_R1_001.fastq.gz RNA-Seq 424.8 MB link
— Day_7_Control_2_S27_L008_R1_001.fastq.gz RNA-Seq 613.2 MB link
— Day_7_Control_2_S28_L008_R1_001.fastq.gz RNA-Seq 525.5 MB link
— Day_7_MALAT1_1_S21_L008_R1_001.fastq.gz RNA-Seq 539.2 MB link
— Day_7_MALAT1_1_S22_L008_R1_001.fastq.gz RNA-Seq 727.0 MB link
— Day_7_MALAT1_1_S23_L008_R1_001.fastq.gz RNA-Seq 505.4 MB link
— Day_7_MALAT1_1_S24_L008_R1_001.fastq.gz RNA-Seq 484.0 MB link
— Day_7_MALAT1_2_S29_L008_R1_001.fastq.gz RNA-Seq 612.0 MB link
— Day_7_MALAT1_2_S30_L008_R1_001.fastq.gz RNA-Seq 445.0 MB link
— Day_7_MALAT1_2_S31_L008_R1_001.fastq.gz RNA-Seq 793.5 MB link
— Day_7_MALAT1_2_S32_L008_R1_001.fastq.gz RNA-Seq 644.1 MB link
— SRR19217837_GSM6153601 RNA-Seq 672.0 MB link
— SRR19217838_GSM6153601 RNA-Seq 424.0 MB link
— SRR19217839_GSM6153601 RNA-Seq 613.0 MB link
— SRR19217840_GSM6153601 RNA-Seq 525.0 MB link
— SRR19217841_GSM6153600 RNA-Seq 495.0 MB link
— SRR19217842_GSM6153600 RNA-Seq 532.0 MB link
— SRR19217843_GSM6153600 RNA-Seq 778.0 MB link
— SRR19217844_GSM6153600 RNA-Seq 445.0 MB link
— SRR19217845_GSM6153599 RNA-Seq 612.0 MB link
— SRR19217846_GSM6153599 RNA-Seq 445.0 MB link
— SRR19217847_GSM6153599 RNA-Seq 793.0 MB link
— SRR19217848_GSM6153599 RNA-Seq 644.0 MB link
— SRR19217848.lite RNA-Seq 644.1 MB link
— SRR19217849_GSM6153598 RNA-Seq 539.0 MB link
— SRR19217850_GSM6153598 RNA-Seq 726.0 MB link
— SRR19217851_GSM6153598 RNA-Seq 505.0 MB link
— SRR19217852_GSM6153598 RNA-Seq 483.0 MB link