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GSE253825

GSE GEO
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Nonsense-mediated mRNA decay counteracts TRP53 to maintain the progenitor cell pool for brain development (snRNA-seq_e15invivo)

Organism: Mus musculus
Platform: GPL21103
Samples: 2
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jan 21 2024
Last Updated: Sep 09 2024
Status: Public on May 31 2024
Contact: Sika,,Zheng (University of California, Riverside)

Relations

SubSeries of: GSE220462 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1067336

Summary

To examine the transcriptomic changes in neocorices from E13.5 Emx1-Upf2cKO and their control littermates at a single cell level, we performed snRNA-seq using the 10x Chromium platform.

Overall Design

Comparative gene expression profiling analysis of snRNA-seq data for neocorices from E15.5 Emx1-Upf2cKO and their control littermates.

Analysis (1 step)

View Data Processing
Processing steps for GSE253825
  1. STAR (version 2.7.11a, reference genome: mm10-2020-A<based on Gencode vM23, and filtering out pseudogenes, TEC, miRNA etc. a total of 32285 genes) was used to perform alignment, filtering, barcode counting, and UMI counting for single cell RNA-Seq.

Supplementary Files (1)

GSE253825_RAW.tar Download
GEO Samples (2)
GSM8028390 GSM8028391

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 (2) and Runs (4)

Total: 119387 MB
SRX23341435 SRP485053 RNA-Seq PAIRED
GSM8028390: E15.5 Upf2fl/fl Emx1-Cre- mouse cortex; Mus musculus; RNA-Seq
Sample: SRS20203586
BioProject: PRJNA1067336
BioSample: SAMN39524534
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
genotype: Upf2fl/fl Emx1-Cre-
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR27674090 314669265 94400779500 30091.09 Ctrl_3_AACCGTAA_S1_L001_R1_001.fastq.gz, Ctrl_3_AACCGTAA_S1_L001_R2_0… SRA
SRR27674091 329639271 98891781300 31550.29 Ctrl_3_TCGGCGTC_S1_L001_R1_001.fastq.gz, Ctrl_3_TCGGCGTC_S1_L001_R2_0… SRA
SRX23341436 SRP485053 RNA-Seq PAIRED
GSM8028391: E15.5 Upf2fl/fl Emx1-Cre+ mouse cortex; Mus musculus; RNA-Seq
Sample: SRS20203587
BioProject: PRJNA1067336
BioSample: SAMN39524533
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
genotype: Upf2fl/fl Emx1-Cre+
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR27674088 289112799 86733839700 28025.96 KO_1_CTAAACGG_S1_L001_R1_001.fastq.gz, KO_1_CTAAACGG_S1_L001_R2_001.f… SRA
SRR27674089 307440457 92232137100 29719.66 KO_1_GGTTTACT_S1_L001_R1_001.fastq.gz, KO_1_GGTTTACT_S1_L001_R2_001.f… 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
— Ctrl_3_AACCGTAA_S1_L001_R1_001.fastq.gz RNA-Seq 29.4 GB link
— Ctrl_3_TCGGCGTC_S1_L001_R1_001.fastq.gz RNA-Seq 30.8 GB link
— KO_1_CTAAACGG_S1_L001_R1_001.fastq.gz RNA-Seq 27.4 GB link
— KO_1_GGTTTACT_S1_L001_R1_001.fastq.gz RNA-Seq 29.0 GB link