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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 (2)

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

Data Files (4)

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