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GSE203090

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

Organism: Mus musculus
Platform: GPL21103
Samples: 10
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/PRJNA838562

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 (3 steps)

View Data Processing
Processing steps for GSE203090
  1. Libraries were filtered and mapped to the mm10 genome using ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline with default parameters for histone marks (github.com/ENCODE-DCC/chip-seq-pipeline2).
  2. Final pooled bigwig files were used for visualization.
  3. none provided by the submitter

Supplementary Files (4)

GSE203090_H3K27me3.Malat1.fc.signal.bigwig Download
GSE203090_H3K27me3.NT.fc.signal.bigwig Download
GSE203090_H3K4me3.Malat1.fc.signal.bigwig Download
GSE203090_H3K4me3.NT.fc.signal.bigwig Download
GEO Samples (10)
GSM6153693 GSM6153694 GSM6153695 GSM6153696 GSM6153697 GSM6153698 GSM6153699 GSM6153700 GSM6153701 GSM6153702

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 (10) and Runs (40)

Total: 16801 MB
SRX15281945 SRP375362 ChIP-Seq SINGLE
GSM6153693: Day7 H3K27me3 Malat1 Knockdown, replicate 1, ChIP-seq; Mus musculus; ChIP-Seq
Sample: SRS13013345
BioProject: PRJNA838562
BioSample: SAMN28448375
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
SRR19218025 8973901 682016476 247.08 MALAT1_A1_H3K27me3_S1_L005_R1_001.fastq.gz, SRR19218025, SRR19218025.… SRA
SRR19218026 8827707 670905732 244.2 MALAT1_A1_H3K27me3_S1_L006_R1_001.fastq.gz, SRR19218026, SRR19218026.… SRA
SRR19218027 34922177 2654085452 1005.61 MALAT1_A1_H3K27me3_S1_L007_R1_001.fastq.gz, SRR19218027, SRR19218027.… SRA
SRR19218028 35328981 2685002556 1026.79 MALAT1_A1_H3K27me3_S1_L008_R1_001.fastq.gz, SRR19218028, SRR19218028.… SRA
SRX15281946 SRP375362 ChIP-Seq SINGLE
GSM6153694: Day7 H3K27me3 Malat1 Knockdown, replicate 2, ChIP-seq; Mus musculus; ChIP-Seq
Sample: SRS13013346
BioProject: PRJNA838562
BioSample: SAMN28448374
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
SRR19218021 7834300 595406800 223.72 MALAT1_A2_H3K27me3_S2_L005_R1_001.fastq.gz, SRR19218021, SRR19218021.… SRA
SRR19218022 7757252 589551152 222.06 MALAT1_A2_H3K27me3_S2_L006_R1_001.fastq.gz, SRR19218022, SRR19218022.… SRA
SRR19218023 37327050 2836855800 1115.91 MALAT1_A2_H3K27me3_S2_L007_R1_001.fastq.gz, SRR19218023, SRR19218023.… SRA
SRR19218024 37818047 2874171572 1139.72 MALAT1_A2_H3K27me3_S2_L008_R1_001.fastq.gz, SRR19218024, SRR19218024.… SRA
SRX15281947 SRP375362 ChIP-Seq SINGLE
GSM6153695: Day7 H3K27me3 Nontarget Knockdown, replicate 1, ChIP-seq; Mus musculus; ChIP-Seq
Sample: SRS13013347
BioProject: PRJNA838562
BioSample: SAMN28448373
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
SRR19218017 23068372 1753196272 682.39 NT_1_H3K27me3_S4_L007_R1_001.fastq.gz, SRR19218017, SRR19218017.lite SRA
SRR19218018 23298598 1770693448 693.85 NT_1_H3K27me3_S4_L008_R1_001.fastq.gz, SRR19218018, SRR19218018.lite SRA
SRR19218019 4687198 356227048 134.15 NT_1_H3K27me3_S6_L005_R1_001.fastq.gz, SRR19218019, SRR19218019.lite SRA
SRR19218020 4650621 353447196 133.52 NT_1_H3K27me3_S6_L006_R1_001.fastq.gz, SRR19218020, SRR19218020.lite SRA
SRX15281948 SRP375362 ChIP-Seq SINGLE
GSM6153696: Day7 H3K27me3 Nontarget Knockdown, replicate 2, ChIP-seq; Mus musculus; ChIP-Seq
Sample: SRS13013348
BioProject: PRJNA838562
BioSample: SAMN28448372
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
SRR19218013 31817726 2418147176 933.06 NT_2_H3K27me3_S5_L007_R1_001.fastq.gz, SRR19218013, SRR19218013.lite SRA
SRR19218014 32316756 2456073456 956.15 NT_2_H3K27me3_S5_L008_R1_001.fastq.gz, SRR19218014, SRR19218014.lite SRA
SRR19218015 9298913 706717388 256.63 NT_2_H3K27me3_S7_L005_R1_001.fastq.gz, SRR19218015, SRR19218015.lite SRA
SRR19218016 9185518 698099368 254.61 NT_2_H3K27me3_S7_L006_R1_001.fastq.gz, SRR19218016, SRR19218016.lite SRA
SRX15281949 SRP375362 ChIP-Seq SINGLE
GSM6153697: Day7 H3K4me3 Malat1 Knockdown, replicate 1, ChIP-seq; Mus musculus; ChIP-Seq
Sample: SRS13013349
BioProject: PRJNA838562
BioSample: SAMN28448371
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
SRR19218009 5241320 398340320 157.9 MALAT1_A1_H3K4me3_S7_L008_R1_001.fastq.gz, SRR19218009, SRR19218009.l… SRA
SRR19218010 5209560 395926560 155.95 MALAT1_A1_H3K4me3_S7_L007_R1_001.fastq.gz, SRR19218010, SRR19218010.l… SRA
SRR19218011 10726897 815244172 305.97 MALAT1_A1_H3K4me3_S11_L006_R1_001.fastq.gz, SRR19218011, SRR19218011.… SRA
SRR19218012 10875455 826534580 309.33 MALAT1_A1_H3K4me3_S11_L005_R1_001.fastq.gz, SRR19218012, SRR19218012.… SRA
SRX15281950 SRP375362 ChIP-Seq SINGLE
GSM6153698: Day7 H3K4me3 Malat1 Knockdown, replicate 2, ChIP-seq; Mus musculus; ChIP-Seq
Sample: SRS13013350
BioProject: PRJNA838562
BioSample: SAMN28448370
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
SRR19218005 5681390 431785640 172.44 MALAT1_A2_H3K4me3_S9_L008_R1_001.fastq.gz, SRR19218005, SRR19218005.l… SRA
SRR19218006 5614085 426670460 169.09 MALAT1_A2_H3K4me3_S9_L007_R1_001.fastq.gz, SRR19218006, SRR19218006.l… SRA
SRR19218007 11411228 867253328 327.82 MALAT1_A2_H3K4me3_S13_L006_R1_001.fastq.gz, SRR19218007, SRR19218007.… SRA
SRR19218008 11600418 881631768 332.43 MALAT1_A2_H3K4me3_S13_L005_R1_001.fastq.gz, SRR19218008, SRR19218008.… SRA
SRX15281951 SRP375362 ChIP-Seq SINGLE
GSM6153699: Day7 H3K4me3 Nontarget Knockdown, replicate 1, ChIP-seq; Mus musculus; ChIP-Seq
Sample: SRS13013351
BioProject: PRJNA838562
BioSample: SAMN28448369
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
SRR19218001 10665095 810547220 299.19 NT_1_H3K4me3_S16_L006_R1_001.fastq.gz, SRR19218001, SRR19218001.lite SRA
SRR19218002 10751234 817093784 300.7 NT_1_H3K4me3_S16_L005_R1_001.fastq.gz, SRR19218002, SRR19218002.lite SRA
SRR19218003 7149132 543334032 209.93 NT_1_H3K4me3_S10_L008_R1_001.fastq.gz, SRR19218003, SRR19218003.lite SRA
SRR19218004 7112920 540581920 207.54 NT_1_H3K4me3_S10_L007_R1_001.fastq.gz, SRR19218004, SRR19218004.lite SRA
SRX15281952 SRP375362 ChIP-Seq SINGLE
GSM6153700: Day7 H3K4me3 Nontarget Knockdown, replicate 2, ChIP-seq; Mus musculus; ChIP-Seq
Sample: SRS13013352
BioProject: PRJNA838562
BioSample: SAMN28448368
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
SRR19217997 10858496 825245696 300.4 NT_2_H3K4me3_S18_L006_R1_001.fastq.gz, SRR19217997, SRR19217997.lite SRA
SRR19217998 10926731 830431556 300.86 NT_2_H3K4me3_S18_L005_R1_001.fastq.gz, SRR19217998, SRR19217998.lite SRA
SRR19217999 11521292 875618192 330.63 NT_2_H3K4me3_S12_L008_R1_001.fastq.gz, SRR19217999, SRR19217999.lite SRA
SRR19218000 11499528 873964128 328.32 NT_2_H3K4me3_S12_L007_R1_001.fastq.gz, SRR19218000, SRR19218000.lite SRA
SRX15281953 SRP375362 ChIP-Seq SINGLE
GSM6153701: Day7 Malat1 Knockdown no input, ChIP-seq; Mus musculus; ChIP-Seq
Sample: SRS13013353
BioProject: PRJNA838562
BioSample: SAMN28448367
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
SRR19217993 9691101 736523676 269.34 MALAT1_A12_Input_S21_L006_R1_001.fastq.gz, SRR19217993, SRR19217993.l… SRA
SRR19217994 9806625 745303500 271.82 MALAT1_A12_Input_S21_L005_R1_001.fastq.gz, SRR19217994, SRR19217994.l… SRA
SRR19217995 21431488 1628793088 620.63 MALAT1_A12_Input_S13_L008_R1_001.fastq.gz, SRR19217995, SRR19217995.l… SRA
SRR19217996 21219856 1612709056 609.97 MALAT1_A12_Input_S13_L007_R1_001.fastq.gz, SRR19217996, SRR19217996.l… SRA
SRX15281954 SRP375362 ChIP-Seq SINGLE
GSM6153702: Day7 Nontarget no input, ChIP-seq; Mus musculus; ChIP-Seq
Sample: SRS13013354
BioProject: PRJNA838562
BioSample: SAMN28448366
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
SRR19217989 11954887 908571412 324.14 NT_12_Input_S22_L006_R1_001.fastq.gz, SRR19217989, SRR19217989.lite SRA
SRR19217990 11974107 910032132 323.72 NT_12_Input_S22_L005_R1_001.fastq.gz, SRR19217990, SRR19217990.lite SRA
SRR19217991 16038759 1218945684 455.19 NT_12_Input_S14_L008_R1_001.fastq.gz, SRR19217991, SRR19217991.lite SRA
SRR19217992 15909628 1209131728 448.58 NT_12_Input_S14_L007_R1_001.fastq.gz, SRR19217992, SRR19217992.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 (40)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— MALAT1_A12_Input_S13_L007_R1_001.fastq.gz ChIP-Seq 610.0 MB link
— MALAT1_A12_Input_S13_L008_R1_001.fastq.gz ChIP-Seq 620.6 MB link
— MALAT1_A12_Input_S21_L005_R1_001.fastq.gz ChIP-Seq 271.8 MB link
— MALAT1_A12_Input_S21_L006_R1_001.fastq.gz ChIP-Seq 269.3 MB link
— MALAT1_A1_H3K27me3_S1_L005_R1_001.fastq.gz ChIP-Seq 247.1 MB link
— MALAT1_A1_H3K27me3_S1_L006_R1_001.fastq.gz ChIP-Seq 244.2 MB link
— MALAT1_A1_H3K27me3_S1_L007_R1_001.fastq.gz ChIP-Seq 1005.6 MB link
— MALAT1_A1_H3K27me3_S1_L008_R1_001.fastq.gz ChIP-Seq 1.0 GB link
— MALAT1_A1_H3K4me3_S11_L005_R1_001.fastq.gz ChIP-Seq 309.3 MB link
— MALAT1_A1_H3K4me3_S11_L006_R1_001.fastq.gz ChIP-Seq 306.0 MB link
— MALAT1_A1_H3K4me3_S7_L007_R1_001.fastq.gz ChIP-Seq 155.9 MB link
— MALAT1_A1_H3K4me3_S7_L008_R1_001.fastq.gz ChIP-Seq 157.9 MB link
— MALAT1_A2_H3K27me3_S2_L005_R1_001.fastq.gz ChIP-Seq 223.7 MB link
— MALAT1_A2_H3K27me3_S2_L006_R1_001.fastq.gz ChIP-Seq 222.1 MB link
— MALAT1_A2_H3K27me3_S2_L007_R1_001.fastq.gz ChIP-Seq 1.1 GB link
— MALAT1_A2_H3K27me3_S2_L008_R1_001.fastq.gz ChIP-Seq 1.1 GB link
— MALAT1_A2_H3K4me3_S13_L005_R1_001.fastq.gz ChIP-Seq 332.4 MB link
— MALAT1_A2_H3K4me3_S13_L006_R1_001.fastq.gz ChIP-Seq 327.8 MB link
— MALAT1_A2_H3K4me3_S9_L007_R1_001.fastq.gz ChIP-Seq 169.1 MB link
— MALAT1_A2_H3K4me3_S9_L008_R1_001.fastq.gz ChIP-Seq 172.4 MB link
— NT_12_Input_S14_L007_R1_001.fastq.gz ChIP-Seq 448.6 MB link
— NT_12_Input_S14_L008_R1_001.fastq.gz ChIP-Seq 455.2 MB link
— NT_12_Input_S22_L005_R1_001.fastq.gz ChIP-Seq 323.7 MB link
— NT_12_Input_S22_L006_R1_001.fastq.gz ChIP-Seq 324.1 MB link
— NT_1_H3K27me3_S4_L007_R1_001.fastq.gz ChIP-Seq 682.4 MB link
— NT_1_H3K27me3_S4_L008_R1_001.fastq.gz ChIP-Seq 693.8 MB link
— NT_1_H3K27me3_S6_L005_R1_001.fastq.gz ChIP-Seq 134.1 MB link
— NT_1_H3K27me3_S6_L006_R1_001.fastq.gz ChIP-Seq 133.5 MB link
— NT_1_H3K4me3_S10_L007_R1_001.fastq.gz ChIP-Seq 207.5 MB link
— NT_1_H3K4me3_S10_L008_R1_001.fastq.gz ChIP-Seq 209.9 MB link
— NT_1_H3K4me3_S16_L005_R1_001.fastq.gz ChIP-Seq 300.7 MB link
— NT_1_H3K4me3_S16_L006_R1_001.fastq.gz ChIP-Seq 299.2 MB link
— NT_2_H3K27me3_S5_L007_R1_001.fastq.gz ChIP-Seq 933.1 MB link
— NT_2_H3K27me3_S5_L008_R1_001.fastq.gz ChIP-Seq 956.1 MB link
— NT_2_H3K27me3_S7_L005_R1_001.fastq.gz ChIP-Seq 256.6 MB link
— NT_2_H3K27me3_S7_L006_R1_001.fastq.gz ChIP-Seq 254.6 MB link
— NT_2_H3K4me3_S12_L007_R1_001.fastq.gz ChIP-Seq 328.3 MB link
— NT_2_H3K4me3_S12_L008_R1_001.fastq.gz ChIP-Seq 330.6 MB link
— NT_2_H3K4me3_S18_L005_R1_001.fastq.gz ChIP-Seq 300.9 MB link
— NT_2_H3K4me3_S18_L006_R1_001.fastq.gz ChIP-Seq 300.4 MB link