GSE253825
GSE GEONonsense-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
- 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)
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 MBGSM8028390: 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
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
Linked Publications (1)
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.
Data Files (8)
| 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 | |||
| — | SRR27674088_GSM8028391 | RNA-Seq | 27.4 GB | link | |||
| — | SRR27674089_GSM8028391 | RNA-Seq | 29.0 GB | link | |||
| — | SRR27674090_GSM8028390 | RNA-Seq | 29.4 GB | link | |||
| — | SRR27674091_GSM8028390 | RNA-Seq | 30.8 GB | link |