GSE220459
GSE GEOEpistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size (RNA-seq NPC)
Organism:
Mus musculus
Platform:
GPL21103
Samples:
18
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/PRJNA909807
Summary
We performed mRNA-Seq of Upf2 KO, Trp53 KO, and dKO NPC.
Overall Design
Comparative gene expression profiling analysis of RNA-seq data for Upf2 KO, Trp53 KO, and dKO NPC.
Analysis (2 steps)
View Data Processing
Processing steps for GSE220459
- The raw data was mapped using STAR.
- We calculated the gene-level read counts and identified differentially expressed genes by in-house script.
Supplementary Files (1)
GSE220459_NPC_TPM.xlsx
Download
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 (18) and Runs (36)
Total: 86414 MBGSM6805152: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#3, 72 hours [UC_3]; Mus musculus; RNA-Seq
Sample: SRS15996034
BioProject: PRJNA909807
BioSample: SAMN32098097
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: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805153: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#4, 72 hours [UC_4]; Mus musculus; RNA-Seq
Sample: SRS15996035
BioProject: PRJNA909807
BioSample: SAMN32098096
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: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805154: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#5, 72 hours [UC_5]; Mus musculus; RNA-Seq
Sample: SRS15996036
BioProject: PRJNA909807
BioSample: SAMN32098095
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: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805155: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#6, 72 hours [UC_6]; Mus musculus; RNA-Seq
Sample: SRS15996037
BioProject: PRJNA909807
BioSample: SAMN32098094
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: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805156: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#8, 72 hours [UC_8]; Mus musculus; RNA-Seq
Sample: SRS15996038
BioProject: PRJNA909807
BioSample: SAMN32098093
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: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805157: Upf2fl/fl NPCs, AAV9-Cre treatment biol rep#9, 72 hours [UC_9]; Mus musculus; RNA-Seq
Sample: SRS15996039
BioProject: PRJNA909807
BioSample: SAMN32098092
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: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805158: Upf2fl/fl NPCs, No treatment biol rep#3, 72 hours [UM_3]; Mus musculus; RNA-Seq
Sample: SRS15996040
BioProject: PRJNA909807
BioSample: SAMN32098091
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: Mock
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805159: Upf2fl/fl NPCs, No treatment biol rep#4, 72 hours [UM_4]; Mus musculus; RNA-Seq
Sample: SRS15996041
BioProject: PRJNA909807
BioSample: SAMN32098090
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: Mock
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805160: Upf2fl/fl NPCs, No treatment biol rep#5, 72 hours [UM_5]; Mus musculus; RNA-Seq
Sample: SRS15996042
BioProject: PRJNA909807
BioSample: SAMN32098089
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: Mock
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805161: Upf2fl/fl NPCs, No treatment biol rep#6, 72 hours [UM_6]; Mus musculus; RNA-Seq
Sample: SRS15996043
BioProject: PRJNA909807
BioSample: SAMN32098088
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: Mock
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805162: Upf2fl/fl NPCs, No treatment biol rep#8, 72 hours [UM_8]; Mus musculus; RNA-Seq
Sample: SRS15996044
BioProject: PRJNA909807
BioSample: SAMN32098087
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: Mock
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805163: Upf2fl/fl NPCs, No treatment biol rep#9, 72 hours [UM_9]; Mus musculus; RNA-Seq
Sample: SRS15996045
BioProject: PRJNA909807
BioSample: SAMN32098086
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: Mock
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805164: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#3, 72 hours [UP_C3]; Mus musculus; RNA-Seq
Sample: SRS15996046
BioProject: PRJNA909807
BioSample: SAMN32098085
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl Trp53fl/fl
treatment: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805165: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#4, 72 hours [UP_C4]; Mus musculus; RNA-Seq
Sample: SRS15996047
BioProject: PRJNA909807
BioSample: SAMN32098084
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl Trp53fl/fl
treatment: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805166: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#5, 72 hours [UP_C5]; Mus musculus; RNA-Seq
Sample: SRS15996048
BioProject: PRJNA909807
BioSample: SAMN32098083
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl Trp53fl/fl
treatment: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805167: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#6, 72 hours [UP_C6]; Mus musculus; RNA-Seq
Sample: SRS15996049
BioProject: PRJNA909807
BioSample: SAMN32098082
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl Trp53fl/fl
treatment: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805168: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#8, 72 hours [UP_C8]; Mus musculus; RNA-Seq
Sample: SRS15996050
BioProject: PRJNA909807
BioSample: SAMN32098081
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl Trp53fl/fl
treatment: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
GSM6805169: Upf2fl/fl Trp53fl/fl NPCs, AAV9-Cre treatment biol rep#9, 72 hours [UP_C9]; Mus musculus; RNA-Seq
Sample: SRS15996051
BioProject: PRJNA909807
BioSample: SAMN32098080
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Mus musculus
Sample attributes
source_name: Cortex
tissue: Cortex
cell type: Neural progenitor cells
genotype: Upf2fl/fl Trp53fl/fl
treatment: AAV9-Cre infection
strain background: C57BL/6
geo_loc_name: missing
collection_date: missing
Original files (1)
Cortex
Linked Publications (2)
Data Files (36)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | UC_3_CKDL220004752-1a-3_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 1.9 GB | link | |||
| — | UC_3_CKDL220004752-1a-3_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.1 GB | link | |||
| — | UC_4_CKDL220004752-1a-11_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.5 GB | link | |||
| — | UC_4_CKDL220004752-1a-11_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.7 GB | link | |||
| — | UC_5_CKDL220004752-1a-23_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.5 GB | link | |||
| — | UC_5_CKDL220004752-1a-23_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.7 GB | link | |||
| — | UC_6_CKDL220004752-1a-4_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 1.9 GB | link | |||
| — | UC_6_CKDL220004752-1a-4_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.1 GB | link | |||
| — | UC_8_CKDL220004752-1a-12_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.4 GB | link | |||
| — | UC_8_CKDL220004752-1a-12_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.6 GB | link | |||
| — | UC_9_CKDL220004752-1a-16_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.4 GB | link | |||
| — | UC_9_CKDL220004752-1a-16_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.6 GB | link | |||
| — | UM_3_CKDL220004752-1a-1_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.0 GB | link | |||
| — | UM_3_CKDL220004752-1a-1_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.2 GB | link | |||
| — | UM_4_CKDL220004752-1a-10_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.4 GB | link | |||
| — | UM_4_CKDL220004752-1a-10_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.6 GB | link | |||
| — | UM_5_CKDL220004752-1a-22_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.0 GB | link | |||
| — | UM_5_CKDL220004752-1a-22_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.1 GB | link | |||
| — | UM_6_CKDL220004752-1a-2_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.4 GB | link | |||
| — | UM_6_CKDL220004752-1a-2_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.6 GB | link | |||
| — | UM_8_CKDL220004752-1a-7_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.2 GB | link | |||
| — | UM_8_CKDL220004752-1a-7_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.3 GB | link | |||
| — | UM_9_CKDL220004752-1a-15_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.0 GB | link | |||
| — | UM_9_CKDL220004752-1a-15_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.2 GB | link | |||
| — | UP_C3_CKDL220004752-1a-9_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 1.8 GB | link | |||
| — | UP_C3_CKDL220004752-1a-9_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 1.9 GB | link | |||
| — | UP_C4_CKDL220004752-1a-21_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.1 GB | link | |||
| — | UP_C4_CKDL220004752-1a-21_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.3 GB | link | |||
| — | UP_C5_CKDL220004752-1a-27_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.1 GB | link | |||
| — | UP_C5_CKDL220004752-1a-27_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.2 GB | link | |||
| — | UP_C6_CKDL220004752-1a-6_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 2.1 GB | link | |||
| — | UP_C6_CKDL220004752-1a-6_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.3 GB | link | |||
| — | UP_C8_CKDL220004752-1a-14_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 3.9 GB | link | |||
| — | UP_C8_CKDL220004752-1a-14_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 4.2 GB | link | |||
| — | UP_C9_CKDL220004752-1a-19_HHJT3BBXX_L8_1.fq.gz | RNA-Seq | 1.8 GB | link | |||
| — | UP_C9_CKDL220004752-1a-19_HHJWLBBXX_L1_1.fq.gz | RNA-Seq | 2.0 GB | link |