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GSE203089

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

Organism: Mus musculus
Platform: GPL21103
Samples: 2
Experiment Types:
Other
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/PRJNA838563

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 (19 steps)

View Data Processing
Processing steps for GSE203089
  1. Reads were trimmed with cutadapt -l 86 --max-n 5 -o (v1.18), mapped to RNA-Linker-DNA (GTTGGATTCNNNGACACAGCTCACTCCCACACACCGAACTCCAAC) with bwa mem -k 5 -L 4 -B 2 -O 4 (v0.7.15) and sorted with samtools sort (v1.7).
  2. RNA and DNA reads were separated with GridTools matefq (https://github.com/biz007/gridtools).
  3. Reads were then mapped to the mm10 genome with bwa mem -k 17 -w 1 -T 1.
  4. GridTools evaluate was then used to correct against background and RNA-DNA mate read pair quality and quantity with bin size of 1 kb and moving windows of 10.
  5. GridTools.py evaluate function uses a gene annotation GTF (Gene transfer format) file to ensure that RNA end of the read always uniquely maps to its correct chromosomal location.
  6. Thus, during the analysis, only RNA reads that map back to its own locus will be retained.
  7. Moreover, the DNA end of the read will also be unique mapped, ensuring that both the RNA and DNA ends of each read are all unique reads.
  8. No read that maps to multiple locations in the genome (including repeat elements all over chromosomes) will be retained during analysis.
Showing first 8 steps.

Supplementary Files (1)

GSE203089_RAW.tar Download
GEO Samples (2)
GSM6153691 GSM6153692

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 (2) and Runs (12)

Total: 37301 MB
SRX15282048 SRP375365 OTHER SINGLE
GSM6153691: D4.5 WT CD8, replicate 1, GRID-seq; Mus musculus; OTHER
Sample: SRS13013447
BioProject: PRJNA838563
BioSample: SAMN28448738
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 (6)
Run Spots Bases Size (MB) Files Link
SRR19218128 55541331 5554133100 2059.63 CD8_Day4_1_S5_L005_R1_001.fastq.gz, SRR19218128, SRR19218128.lite SRA
SRR19218129 54834538 5483453800 2060.46 CD8_Day4_1_S5_L006_R1_001.fastq.gz, SRR19218129, SRR19218129.lite SRA
SRR19218130 54173349 5417334900 2024.26 CD8_Day4_1_S5_L007_R1_001.fastq.gz, SRR19218130, SRR19218130.lite SRA
SRR19218131 52942678 5294267800 1997.13 CD8_Day4_1_S5_L008_R1_001.fastq.gz, SRR19218131, SRR19218131.lite SRA
SRR19218132 177510861 17928596961 5240.07 CD8_Day4_1_S5_L001_R1_001.fastq.gz, SRR19218132, SRR19218132.lite SRA
SRR19218133 181905613 18372466913 5394.53 CD8_Day4_1_S5_L002_R1_001.fastq.gz, SRR19218133, SRR19218133.lite SRA
SRX15282049 SRP375365 OTHER SINGLE
GSM6153692: D4.5 WT CD8, replicate 2, GRID-seq; Mus musculus; OTHER
Sample: SRS13013448
BioProject: PRJNA838563
BioSample: SAMN28448737
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 (6)
Run Spots Bases Size (MB) Files Link
SRR19218122 78996906 7899690600 2910.18 CD8_Day4_2_S6_L005_R1_001.fastq.gz, SRR19218122, SRR19218122.lite SRA
SRR19218123 77840017 7784001700 2903.46 CD8_Day4_2_S6_L006_R1_001.fastq.gz, SRR19218123, SRR19218123.lite SRA
SRR19218124 76975946 7697594600 2858.25 CD8_Day4_2_S6_L007_R1_001.fastq.gz, SRR19218124, SRR19218124.lite SRA
SRR19218125 75161864 7516186400 2817.23 CD8_Day4_2_S6_L008_R1_001.fastq.gz, SRR19218125, SRR19218125.lite SRA
SRR19218126 116363948 11752758748 3473.65 CD8_Day4_2_S6_L001_R1_001.fastq.gz, SRR19218126, SRR19218126.lite SRA
SRR19218127 118814507 12000265207 3562.07 CD8_Day4_2_S6_L002_R1_001.fastq.gz, SRR19218127, SRR19218127.lite 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 (12)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— CD8_Day4_1_S5_L001_R1_001.fastq.gz OTHER 5.1 GB link
— CD8_Day4_1_S5_L002_R1_001.fastq.gz OTHER 5.3 GB link
— CD8_Day4_1_S5_L005_R1_001.fastq.gz OTHER 2.0 GB link
— CD8_Day4_1_S5_L006_R1_001.fastq.gz OTHER 2.0 GB link
— CD8_Day4_1_S5_L007_R1_001.fastq.gz OTHER 2.0 GB link
— CD8_Day4_1_S5_L008_R1_001.fastq.gz OTHER 2.0 GB link
— CD8_Day4_2_S6_L001_R1_001.fastq.gz OTHER 3.4 GB link
— CD8_Day4_2_S6_L002_R1_001.fastq.gz OTHER 3.5 GB link
— CD8_Day4_2_S6_L005_R1_001.fastq.gz OTHER 2.8 GB link
— CD8_Day4_2_S6_L006_R1_001.fastq.gz OTHER 2.8 GB link
— CD8_Day4_2_S6_L007_R1_001.fastq.gz OTHER 2.8 GB link
— CD8_Day4_2_S6_L008_R1_001.fastq.gz OTHER 2.8 GB link