GSE203091
GSE GEOThe long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression (CUT&RUN)
Organism:
Mus musculus
Platform:
GPL24247
Samples:
12
Experiment Types:
Genome binding/occupancy 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/PRJNA838561
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 (6 steps)
View Data Processing
Processing steps for GSE203091
- Reads were mapped either to the mouse or yeast genome with bowtie2 -p 8 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 (v1.2.2).
- Mapped reads were then converted into bed files.
- A scale factor for Spike-In normalization was calculated for each sample by dividing 1000 from the sequencing depth of mapped yeast reads.
- Bed files were normalized using bedtools genomcov (v2.29.2) with the respective scaling factor calculated as describe above.
- Peaks calls were determined using macs2 macs2 callpeak -broad --broad-cutoff 0.1 -B --nomodel --keep-dup all -f BED (v2.1.2).
- none provided by the submitter
Supplementary Files (1)
GSE203091_RAW.tar
Download
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 (12) and Runs (12)
Total: 16063 MBGSM6153703: Day7 TE Malat1 Knockdown, replicate 1, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015078
BioProject: PRJNA838561
BioSample: SAMN28448736
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221357 | 33690043 | 6784872300 | 1982.91 | Malat1_TE_1.R1.fastq, Malat1_TE_1.R2.fastq, SRR19221357, SRR19221357.… | SRA |
GSM6153704: Day7 TE Malat1 Knockdown, replicate 2, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015079
BioProject: PRJNA838561
BioSample: SAMN28448735
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221356 | 36177893 | 7286351802 | 2132.11 | Malat1_TE_2.R1.fastq, Malat1_TE_2.R2.fastq, SRR19221356, SRR19221356.… | SRA |
GSM6153705: Day7 TE Nontarget Knockdown, replicate 1, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015081
BioProject: PRJNA838561
BioSample: SAMN28448734
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221355 | 30168816 | 6088904765 | 1763.07 | NT_TE_1.R1.fastq, NT_TE_1.R2.fastq, SRR19221355, SRR19221355.lite | SRA |
GSM6153706: Day7 TE Nontarget Knockdown, replicate 2, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015080
BioProject: PRJNA838561
BioSample: SAMN28448733
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221354 | 27679160 | 5586574342 | 1613.61 | NT_TE_2.R1.fastq, NT_TE_2.R2.fastq, SRR19221354, SRR19221354.lite | SRA |
GSM6153707: Day7 MP Malat1 Knockdown, replicate 1, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015082
BioProject: PRJNA838561
BioSample: SAMN28448732
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221353 | 32215490 | 6502696111 | 1883.42 | Malat1_MP_1.R1.fastq, Malat1_MP_1.R2.fastq, SRR19221353, SRR19221353.… | SRA |
GSM6153708: Day7 MP Malat1 Knockdown, replicate 2, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015083
BioProject: PRJNA838561
BioSample: SAMN28448731
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221352 | 34699409 | 7003943206 | 2032.76 | Malat1_MP_2.R1.fastq, Malat1_MP_2.R2.fastq, SRR19221352, SRR19221352.… | SRA |
GSM6153709: Day7 MP Nontarget Knockdown, replicate 1, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015084
BioProject: PRJNA838561
BioSample: SAMN28448730
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221351 | 21303344 | 4300728213 | 1239.48 | NT_MP_1.R1.fastq, NT_MP_1.R2.fastq, SRR19221351, SRR19221351.lite | SRA |
GSM6153710: Day7 MP Nontarget Knockdown, replicate 2, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015085
BioProject: PRJNA838561
BioSample: SAMN28448729
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221350 | 23799420 | 4804540967 | 1388.18 | NT_MP_2.R1.fastq, NT_MP_2.R2.fastq, SRR19221350, SRR19221350.lite | SRA |
GSM6153711: Day7 TE Malat1 Knockdown isotype, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015086
BioProject: PRJNA838561
BioSample: SAMN28448728
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221349 | 7010698 | 1411801696 | 419.46 | Malat1_TE_iso.R1.fastq, Malat1_TE_iso.R2.fastq, SRR19221349, SRR19221… | SRA |
GSM6153712: Day7 TE Nontarget Knockdown isotype, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015087
BioProject: PRJNA838561
BioSample: SAMN28448727
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221348 | 7811261 | 1576778193 | 471.45 | NT_TE_iso.R1.fastq, NT_TE_iso.R2.fastq, SRR19221348, SRR19221348.lite | SRA |
GSM6153713: Day7 MP Malat1 Knockdown isotype, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015088
BioProject: PRJNA838561
BioSample: SAMN28448726
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221347 | 7133648 | 1440163358 | 430.31 | NT_Malat1_iso.R1.fastq, NT_Malat1_iso.R2.fastq, SRR19221347, SRR19221… | SRA |
GSM6153714: Day7 MP Nontarget Knockdown isotype, CUT&RUN; Mus musculus; OTHER
Sample: SRS13015089
BioProject: PRJNA838561
BioSample: SAMN28448725
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
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 (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR19221346 | 11773562 | 2377068662 | 706.5 | NT_MP_iso.R1.fastq, NT_MP_iso.R2.fastq, SRR19221346, SRR19221346.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 (13)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | Malat1_MP_1.R1.fastq | OTHER | 1.8 GB | link | |||
| — | Malat1_MP_2.R1.fastq | OTHER | 2.0 GB | link | |||
| — | Malat1_TE_1.R1.fastq | OTHER | 1.9 GB | link | |||
| — | Malat1_TE_2.R1.fastq | OTHER | 2.1 GB | link | |||
| — | Malat1_TE_iso.R1.fastq | OTHER | 419.5 MB | link | |||
| — | NT_Malat1_iso.R1.fastq | OTHER | 430.3 MB | link | |||
| — | NT_MP_1.R1.fastq | OTHER | 1.2 GB | link | |||
| — | NT_MP_2.R1.fastq | OTHER | 1.4 GB | link | |||
| — | NT_MP_iso.R1.fastq | OTHER | 706.5 MB | link | |||
| — | NT_TE_1.R1.fastq | OTHER | 1.7 GB | link | |||
| — | NT_TE_2.R1.fastq | OTHER | 1.6 GB | link | |||
| — | NT_TE_iso.R1.fastq | OTHER | 471.4 MB | link | |||
| — | SRR19221352.lite | OTHER | 2.0 GB | link |