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GSE220460

GSE GEO
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Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size (RNA-seq e13invivo)

Organism: Mus musculus
Platform: GPL21103
Samples: 4
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Dec 07 2022
Last Updated: May 30 2024
Status: Public on May 30 2024
Contact: Sika,,Zheng (University of California, Riverside)

Relations

SubSeries of: GSE220462 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA909808

Summary

To determine the transcriptomic impacts of NMD on lineage transition in vivo, we performed mRNA-Seq of neocortices from E13.5 Emx1-Upf2cKO and their control littermates.

Overall Design

Comparative gene expression profiling analysis of RNA-seq data for neocorices from E13.5 Emx1-Upf2cKO and their control littermates.

Analysis (2 steps)

View Data Processing
Processing steps for GSE220460
  1. The raw data was mapped using STAR.
  2. We calculated the gene-level read counts and identified differentially expressed genes by in-house script.

Supplementary Files (1)

GSE220460_e13invivo_TPM.xlsx Download
GEO Samples (4)
GSM6805170 GSM6805171 GSM6805172 GSM6805173

Dataset Citations (1)

Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size.
PMID 38697111 · 2024 · Neuron
Lin Lin, Jingrong Zhao, Naoto Kubota, Zhelin Li, Yi-Li Lam, Lauren P Nguyen, Lu Yang, Sheela P Pokharel, Steven M Blue, Brian A Yee, Renee Chen, Gene W Yeo, Chun-Wei Chen, Liang Chen, Sika Zheng

SRA Experiments (4) and Runs (4)

Total: 21612 MB
SRX18530119 SRP411870 RNA-Seq PAIRED
GSM6805170: E13.5 Upf2fl/fl Emx1-Cre+ mouse cortex [Emxi_4]; Mus musculus; RNA-Seq
Sample: SRS15995743
BioProject: PRJNA909808
BioSample: SAMN32097652
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
developmental stage: E13.5
genotype: Upf2fl/fl Emx1-Cre+
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566922 41322526 12396757800 4721.69 Emxi_4_CKDL200155779-1a-3_HC3L5BBXX_L6_1.fq.gz, Emxi_4_CKDL200155779-… SRA
SRX18530120 SRP411870 RNA-Seq PAIRED
GSM6805171: E13.5 Upf2fl/fl Emx1-Cre+ mouse cortex [Emxi_5]; Mus musculus; RNA-Seq
Sample: SRS15995744
BioProject: PRJNA909808
BioSample: SAMN32097651
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
developmental stage: E13.5
genotype: Upf2fl/fl Emx1-Cre+
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566921 46052835 13815850500 5162.64 Emxi_5_CKDL200155779-1a-8_HC3L5BBXX_L6_1.fq.gz, Emxi_5_CKDL200155779-… SRA
SRX18530121 SRP411870 RNA-Seq PAIRED
GSM6805172: E13.5 Upf2fl/+ Emx1-Cre- mouse cortex [Emxi_8]; Mus musculus; RNA-Seq
Sample: SRS15995745
BioProject: PRJNA909808
BioSample: SAMN32097650
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
developmental stage: E13.5
genotype: Upf2fl/+ Emx1-Cre-
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566920 54148908 16244672400 6093.54 Emxi_8_CKDL200155779-1a-10_HC3L5BBXX_L6_1.fq.gz, Emxi_8_CKDL200155779… SRA
SRX18530122 SRP411870 RNA-Seq PAIRED
GSM6805173: E13.5 Upf2fl/+ Emx1-Cre- mouse cortex [Emxi_9]; Mus musculus; RNA-Seq
Sample: SRS15995746
BioProject: PRJNA909808
BioSample: SAMN32097649
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
developmental stage: E13.5
genotype: Upf2fl/+ Emx1-Cre-
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566919 49653759 14896127700 5634.24 Emxi_9_CKDL200155779-1a-11_HC3L5BBXX_L6_1.fq.gz, Emxi_9_CKDL200155779… SRA

Linked Publications (1)

Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size.
Neuron · 2024

Potentially Related Publications (1)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size.
Neuron · 2024

Data Files (8)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— Emxi_4_CKDL200155779-1a-3_HC3L5BBXX_L6_1.fq.gz RNA-Seq 4.6 GB link
— Emxi_5_CKDL200155779-1a-8_HC3L5BBXX_L6_1.fq.gz RNA-Seq 5.0 GB link
— Emxi_8_CKDL200155779-1a-10_HC3L5BBXX_L6_1.fq.gz RNA-Seq 6.0 GB link
— Emxi_9_CKDL200155779-1a-11_HC3L5BBXX_L6_1.fq.gz RNA-Seq 5.5 GB link
— SRR22566919_GSM6805173 RNA-Seq 5.5 GB link
— SRR22566920_GSM6805172 RNA-Seq 6.0 GB link
— SRR22566921_GSM6805171 RNA-Seq 5.0 GB link
— SRR22566922_GSM6805170 RNA-Seq 4.6 GB link