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GSE145430

GSE GEO
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Identifying differentially expressed genes in Zmat3 knockout cells

Organism: Mus musculus
Platform: GPL13112
Samples: 6
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Feb 18 2020
Last Updated: Nov 06 2020
Status: Public on Nov 06 2020
Contact: Kathryn,,Bieging-Rolett (Stanford University School of Medicine)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA607207 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP249789

Summary

The goal of the study was to identify genes whose expression is Zmat3 depedent using RNA-seq.

Overall Design

We used CRISPR/Cas9 to knockout Zmat3 in Cas9+ E1A;HrasG12V mouse embryonic fibroblasts (MEFs). After selection for Zmat3 or negative control sgRNAs, cells were cultured for 10 days, and then RNA was collected for RNA-seq, using Illumina TruSeq v2.

Analysis (2 steps)

View Data Processing
Processing steps for GSE145430
  1. RNA-seq reads were aligned to the mouse genome (mm10) and analyzed using the public server Galaxy (usegalaxy.org), which employs the STAR aligner.
  2. DESeq2 was used for differential expression analysis

Supplementary Files (1)

GSE145430_all_DEseq2_Zmat3_processed_data.xlsx Download
GEO Samples (6)
GSM4318351 GSM4318352 GSM4318353 GSM4318354 GSM4318355 GSM4318356

SRA Experiments (6) and Runs (6)

Total: 13914 MB
SRX7737617 SRP249789 RNA-Seq PAIRED
GSM4318351: Control 1; Mus musculus; RNA-Seq
Sample: SRS6157691
BioProject: PRJNA607207
BioSample: SAMN14124288
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Mouse embryonic fibroblasts
genotype: Cas9+;E1A;HrasG12V
sgrna: sgNegative control EV
cell type: embryonic fibroblasts
Original files (1)
Mouse embryonic fibroblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11098972 54301490 4325957544 1649.28 KB1-CGATGT_S1_L001_R1_001.fastq.gz, KB1-CGATGT_S1_L001_R2_001.fastq.g… SRA
SRX7737618 SRP249789 RNA-Seq PAIRED
GSM4318352: Control 2; Mus musculus; RNA-Seq
Sample: SRS6157692
BioProject: PRJNA607207
BioSample: SAMN14124287
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Mouse embryonic fibroblasts
genotype: Cas9+;E1A;HrasG12V
sgrna: sgNegative control SPA
cell type: embryonic fibroblasts
Original files (1)
Mouse embryonic fibroblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11098973 59321801 9016913752 3286.14 KB2-TGACCA_S2_L001_R1_001.fastq.gz, KB2-TGACCA_S2_L001_R2_001.fastq.g… SRA
SRX7737619 SRP249789 RNA-Seq PAIRED
GSM4318353: Control 3; Mus musculus; RNA-Seq
Sample: SRS6157693
BioProject: PRJNA607207
BioSample: SAMN14124286
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Mouse embryonic fibroblasts
genotype: Cas9+;E1A;HrasG12V
sgrna: sgNegative control ACOCA
cell type: embryonic fibroblasts
Original files (1)
Mouse embryonic fibroblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11098974 41648425 6330560600 2332.94 KB4-GCCAAT_S4_L001_R1_001.fastq.gz, KB4-GCCAAT_S4_L001_R2_001.fastq.g… SRA
SRX7737621 SRP249789 RNA-Seq PAIRED
GSM4318354: Zmat3 knockout 1; Mus musculus; RNA-Seq
Sample: SRS6157695
BioProject: PRJNA607207
BioSample: SAMN14124285
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Mouse embryonic fibroblasts
genotype: Cas9+;E1A;HrasG12V
sgrna: sgZmat3 52.6
cell type: embryonic fibroblasts
Original files (1)
Mouse embryonic fibroblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11098975 47288864 7187907328 2623.01 KB5-CAGATC_S5_L001_R1_001.fastq.gz, KB5-CAGATC_S5_L001_R2_001.fastq.g… SRA
SRX7737622 SRP249789 RNA-Seq PAIRED
GSM4318355: Zmat3 knockout 2; Mus musculus; RNA-Seq
Sample: SRS6157696
BioProject: PRJNA607207
BioSample: SAMN14124284
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Mouse embryonic fibroblasts
genotype: Cas9+;E1A;HrasG12V
sgrna: sgZmat3 51.5
cell type: embryonic fibroblasts
Original files (1)
Mouse embryonic fibroblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11098976 36801922 5593892144 2022.83 KB6-CTTGTA_S6_L001_R1_001.fastq.gz, KB6-CTTGTA_S6_L001_R2_001.fastq.g… SRA
SRX7737623 SRP249789 RNA-Seq PAIRED
GSM4318356: Zmat3 knockout 3; Mus musculus; RNA-Seq
Sample: SRS6157697
BioProject: PRJNA607207
BioSample: SAMN14124283
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Mouse embryonic fibroblasts
genotype: Cas9+;E1A;HrasG12V
sgrna: sgZmat3 54.8
cell type: embryonic fibroblasts
Original files (1)
Mouse embryonic fibroblasts
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11098977 35793516 5440614432 2000.0 KB7-AGTCAA_S7_L001_R1_001.fastq.gz, KB7-AGTCAA_S7_L001_R2_001.fastq.g… SRA

Linked Publications (1)

Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.
Molecular cell · 2020

Data Files (6)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— KB1-CGATGT_S1_L001_R1_001.fastq.gz RNA-Seq 1.6 GB link
— KB2-TGACCA_S2_L001_R1_001.fastq.gz RNA-Seq 3.2 GB link
— KB4-GCCAAT_S4_L001_R1_001.fastq.gz RNA-Seq 2.3 GB link
— KB5-CAGATC_S5_L001_R1_001.fastq.gz RNA-Seq 2.6 GB link
— KB6-CTTGTA_S6_L001_R1_001.fastq.gz RNA-Seq 2.0 GB link
— KB7-AGTCAA_S7_L001_R1_001.fastq.gz RNA-Seq 2.0 GB link