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GSE220461

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

Organism: Mus musculus
Platform: GPL21103
Samples: 10
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/PRJNA909810

Summary

To examine the transcriptomic changes in Upf2 KO neural progenitors at a single cell level, we performed scRNA-seq using the 10x Chromium platform.

Overall Design

Upf2 fl/fl NPC were infected with GFP or CRE lentivirus and used for scRNA-seq.

Analysis (1 step)

View Data Processing
Processing steps for GSE220461
  1. Cell Ranger (version 5.0.1, 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)

GSE220461_scRNA-seq_CPM.xlsx Download
GEO Samples (10)
GSM6805174 GSM6805175 GSM6805176 GSM6805177 GSM6805178 GSM6805179 GSM6805180 GSM6805181 GSM6805182 GSM6805183

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 (10) and Runs (10)

Total: 66056 MB
SRX18530123 SRP411871 RNA-Seq PAIRED
GSM6805174: Upf2fl/fl NPCs, GFP lentivirus treatment, 72 hours [GFP_10x_1]; Mus musculus; RNA-Seq
Sample: SRS15995747
BioProject: PRJNA909810
BioSample: SAMN32097583
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl
treatment: GFP-LV infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566930 114004474 35113377992 15746.64 GFP_10x_1_CKDL210009136-1a-SI_GA_E1_HG7NTBBXX_S1_L007_I1_001.fastq.gz… SRA
SRX18530124 SRP411871 RNA-Seq PAIRED
GSM6805175: Upf2fl/fl NPCs, GFP lentivirus treatment, 72 hours [GFP_IDT_1]; Mus musculus; RNA-Seq
Sample: SRS15995748
BioProject: PRJNA909810
BioSample: SAMN32097582
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl
treatment: GFP-LV infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566929 35193022 10557906600 4701.1 GFP_IDT_1_CKDL210009136-1a-AK10633_HG7NTBBXX_L7_1.fq.gz, GFP_IDT_1_CK… SRA
SRX18530125 SRP411871 RNA-Seq PAIRED
GSM6805176: Upf2fl/fl NPCs, GFP lentivirus treatment, 72 hours [GFP_IDT_2]; Mus musculus; RNA-Seq
Sample: SRS15995749
BioProject: PRJNA909810
BioSample: SAMN32097581
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl
treatment: GFP-LV infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566931 32754989 9826496700 4378.17 GFP_IDT_2_CKDL210009136-1a-AK6103_HG7NTBBXX_L7_1.fq.gz, GFP_IDT_2_CKD… SRA
SRX18530126 SRP411871 RNA-Seq PAIRED
GSM6805177: Upf2fl/fl NPCs, GFP lentivirus treatment, 72 hours [GFP_IDT_3]; Mus musculus; RNA-Seq
Sample: SRS15995750
BioProject: PRJNA909810
BioSample: SAMN32097580
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl
treatment: GFP-LV infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566928 38717874 11615362200 5208.41 GFP_IDT_3_CKDL210009136-1a-AK6104_HG7NTBBXX_L7_1.fq.gz, GFP_IDT_3_CKD… SRA
SRX18530127 SRP411871 RNA-Seq PAIRED
GSM6805178: Upf2fl/fl NPCs, GFP lentivirus treatment, 72 hours [GFP_IDT_4]; Mus musculus; RNA-Seq
Sample: SRS15995751
BioProject: PRJNA909810
BioSample: SAMN32097579
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl
treatment: GFP-LV infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566932 40157801 12047340300 5363.48 GFP_IDT_4_CKDL210009136-1a-AK9608_HG7NTBBXX_L7_1.fq.gz, GFP_IDT_4_CKD… SRA
SRX18530128 SRP411871 RNA-Seq PAIRED
GSM6805179: Upf2fl/fl NPCs, Cre lentivirus treatment, 72 hours [CRE_10x_2]; Mus musculus; RNA-Seq
Sample: SRS15995752
BioProject: PRJNA909810
BioSample: SAMN32097578
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl
treatment: CRE-LV infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566925 96837451 29825934908 13361.33 CRE_10x_2_CKDL210009136-1a-SI_GA_E2_HG7NTBBXX_S2_L007_I1_001.fastq.gz… SRA
SRX18530129 SRP411871 RNA-Seq PAIRED
GSM6805180: Upf2fl/fl NPCs, Cre lentivirus treatment, 72 hours [CRE_IDT_1]; Mus musculus; RNA-Seq
Sample: SRS15995753
BioProject: PRJNA909810
BioSample: SAMN32097577
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl
treatment: CRE-LV infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566924 30840657 9252197100 4131.19 CRE_IDT_1_CKDL210009136-1a-AK6102_HG7NTBBXX_L7_1.fq.gz, CRE_IDT_1_CKD… SRA
SRX18530130 SRP411871 RNA-Seq PAIRED
GSM6805181: Upf2fl/fl NPCs, Cre lentivirus treatment, 72 hours [CRE_IDT_2]; Mus musculus; RNA-Seq
Sample: SRS15995755
BioProject: PRJNA909810
BioSample: SAMN32097576
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl
treatment: CRE-LV infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566926 37306022 11191806600 5017.03 CRE_IDT_2_CKDL210009136-1a-AK6101_HG7NTBBXX_L7_1.fq.gz, CRE_IDT_2_CKD… SRA
SRX18530131 SRP411871 RNA-Seq PAIRED
GSM6805182: Upf2fl/fl NPCs, Cre lentivirus treatment, 72 hours [CRE_IDT_3]; Mus musculus; RNA-Seq
Sample: SRS15995754
BioProject: PRJNA909810
BioSample: SAMN32097575
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl
treatment: CRE-LV infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566923 26551370 7965411000 3581.23 CRE_IDT_3_CKDL210009136-1a-AK10638_HG7NTBBXX_L7_1.fq.gz, CRE_IDT_3_CK… SRA
SRX18530132 SRP411871 RNA-Seq PAIRED
GSM6805183: Upf2fl/fl NPCs, Cre lentivirus treatment, 72 hours [CRE_IDT_4]; Mus musculus; RNA-Seq
Sample: SRS15995756
BioProject: PRJNA909810
BioSample: SAMN32097574
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl
treatment: CRE-LV infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22566927 34101104 10230331200 4567.76 CRE_IDT_4_CKDL210009136-1a-AK10639_HG7NTBBXX_L7_1.fq.gz, CRE_IDT_4_CK… 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 (10)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— CRE_10x_2_CKDL210009136-1a-SI_GA_E2_HG7NTBBXX_S2_L007_… RNA-Seq 13.0 GB link
— CRE_IDT_1_CKDL210009136-1a-AK6102_HG7NTBBXX_L7_1.fq.gz RNA-Seq 4.0 GB link
— CRE_IDT_2_CKDL210009136-1a-AK6101_HG7NTBBXX_L7_1.fq.gz RNA-Seq 4.9 GB link
— CRE_IDT_3_CKDL210009136-1a-AK10638_HG7NTBBXX_L7_1.fq.gz RNA-Seq 3.5 GB link
— CRE_IDT_4_CKDL210009136-1a-AK10639_HG7NTBBXX_L7_1.fq.gz RNA-Seq 4.5 GB link
— GFP_10x_1_CKDL210009136-1a-SI_GA_E1_HG7NTBBXX_S1_L007_… RNA-Seq 15.4 GB link
— GFP_IDT_1_CKDL210009136-1a-AK10633_HG7NTBBXX_L7_1.fq.gz RNA-Seq 4.6 GB link
— GFP_IDT_2_CKDL210009136-1a-AK6103_HG7NTBBXX_L7_1.fq.gz RNA-Seq 4.3 GB link
— GFP_IDT_3_CKDL210009136-1a-AK6104_HG7NTBBXX_L7_1.fq.gz RNA-Seq 5.1 GB link
— GFP_IDT_4_CKDL210009136-1a-AK9608_HG7NTBBXX_L7_1.fq.gz RNA-Seq 5.2 GB link