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GSE202202

GSE GEO
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RNA-seq in neurites and soma of primary hippocampal neurons isolated from P0 or P1 mice

Organism: Mus musculus
Platform: GPL19057
Samples: 12
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: May 04 2022
Last Updated: Feb 05 2025
Status: Public on Jan 16 2024
Contact: Celia,,Alecki (McGill University)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA834991

Summary

RNA-seq data on primary neurons isolated from P0 or P1 mice pups after stress using MG132 or under control conditions

Overall Design

Neurons after 17 or 18 days of culture in vitro were stressed using 10 uM of MG132 for 7H. Soma and neurites were isolated and RNA were extracted from each compartment. Single-end RNA sequencing was performed.

Analysis (4 steps)

View Data Processing
Processing steps for GSE202202
  1. Adaptors and sequence with a quality below 20 were removed using trimmomatic (galaxy version 0.38.0)
  2. Reads were aligned on mm10 genome using RNA star (galaxy version 2.7.8a+galaxy0)
  3. Number of reads per transcript was determined using FeatureCounts (galaxy version 2.0.1+galaxy2)
  4. Differential gene expression was determined using DESeq2 (galaxy version 2.11.40.7+galaxy1)

Supplementary Files (1)

GSE202202_RAW.tar Download
GEO Samples (12)
GSM6103821 GSM6103823 GSM6103826 GSM6103827 GSM6103829 GSM6103831 GSM6103833 GSM6103835 GSM6103837 GSM6103839 GSM6103841 GSM6103843

Dataset Citations (2)

PubMed citation (PMID 38168440)
Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis.
PMID 39737952 · 2024 · Nature communications
Célia Alecki, Javeria Rizwan, Phuong Le, Suleima Jacob-Tomas, Mario Fernandez Comaduran, Morgane Verbrugghe, Jia Ming Stella Xu, Sandra Minotti, James Lynch, Jeetayu Biswas, Tad Wu, Heather D Durham, Gene W Yeo, Maria Vera

SRA Experiments (12) and Runs (12)

Total: 5991 MB
SRX15148771 SRP373580 RNA-Seq SINGLE
GSM6103821: Ctrl soma rep1; Mus musculus; RNA-Seq
Sample: SRS12891940
BioProject: PRJNA834991
BioSample: SAMN28088461
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: soma
treatment: Ctrl
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078911 17725078 1329380850 476.16 211012DIV18SomaCtrl_S1_R1_001.fastq.gz, SRR19078911, SRR19078911.lite SRA
SRX15148772 SRP373580 RNA-Seq SINGLE
GSM6103823: Ctrl neurites rep1; Mus musculus; RNA-Seq
Sample: SRS12891939
BioProject: PRJNA834991
BioSample: SAMN28088460
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: neurites
treatment: Ctrl
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078910 11844959 888371925 320.25 211012DIV18DendCtrl_S3_R1_001.fastq.gz, SRR19078910, SRR19078910.lite SRA
SRX15148773 SRP373580 RNA-Seq SINGLE
GSM6103826: MG132 soma rep1; Mus musculus; RNA-Seq
Sample: SRS12891942
BioProject: PRJNA834991
BioSample: SAMN28088459
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: soma
treatment: MG132 10 uM 7H
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078909 14381633 1078622475 385.37 211012DIV18SomaMG132_S2_R1_001.fastq.gz, SRR19078909, SRR19078909.lite SRA
SRX15148774 SRP373580 RNA-Seq SINGLE
GSM6103827: MG132 neurites rep1; Mus musculus; RNA-Seq
Sample: SRS12891941
BioProject: PRJNA834991
BioSample: SAMN28088458
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: neurites
treatment: MG132 10 uM 7H
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078908 12975944 973195800 351.41 211012DIV18DendMG132_S4_R1_001.fastq.gz, SRR19078908, SRR19078908.lite SRA
SRX15148775 SRP373580 RNA-Seq SINGLE
GSM6103829: Ctrl soma rep2; Mus musculus; RNA-Seq
Sample: SRS12891943
BioProject: PRJNA834991
BioSample: SAMN28088457
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: soma
treatment: Ctrl
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078907 12524543 939340725 338.55 211115DIV17SomaCtrl_S5_R1_001.fastq.gz, SRR19078907, SRR19078907.lite SRA
SRX15148776 SRP373580 RNA-Seq SINGLE
GSM6103831: Ctrl neurites rep2; Mus musculus; RNA-Seq
Sample: SRS12891944
BioProject: PRJNA834991
BioSample: SAMN28088456
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: neurites
treatment: Ctrl
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078906 18314496 1373587200 496.14 211115DIV17DendCtrl_S7_R1_001.fastq.gz, SRR19078906, SRR19078906.lite SRA
SRX15148777 SRP373580 RNA-Seq SINGLE
GSM6103833: MG132 soma rep2; Mus musculus; RNA-Seq
Sample: SRS12891945
BioProject: PRJNA834991
BioSample: SAMN28088455
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: soma
treatment: MG132 10 uM 7H
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078905 8484930 636369750 229.85 211115DIV17SomaMG132_S6_R1_001.fastq.gz, SRR19078905, SRR19078905.lite SRA
SRX15148778 SRP373580 RNA-Seq SINGLE
GSM6103835: MG132 neurites rep2; Mus musculus; RNA-Seq
Sample: SRS12891946
BioProject: PRJNA834991
BioSample: SAMN28088454
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: neurites
treatment: MG132 10 uM 7H
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078904 41443612 3108270900 1123.41 211115DIV17DendMG132_S8_R1_001.fastq.gz, SRR19078904, SRR19078904.lite SRA
SRX15148779 SRP373580 RNA-Seq SINGLE
GSM6103837: Ctrl soma rep3; Mus musculus; RNA-Seq
Sample: SRS12891947
BioProject: PRJNA834991
BioSample: SAMN28088453
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: soma
treatment: Ctrl
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078903 15035716 1127678700 405.56 211122DIV17SomaCtrl_S9_R1_001.fastq.gz, SRR19078903, SRR19078903.lite SRA
SRX15148780 SRP373580 RNA-Seq SINGLE
GSM6103839: Ctrl neurites rep3; Mus musculus; RNA-Seq
Sample: SRS12891948
BioProject: PRJNA834991
BioSample: SAMN28088452
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: neurites
treatment: Ctrl
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078902 13530139 1014760425 368.69 211122DIV17DendCtrl_S11_R1_001.fastq.gz, SRR19078902, SRR19078902.lite SRA
SRX15148781 SRP373580 RNA-Seq SINGLE
GSM6103841: MG132 soma rep3; Mus musculus; RNA-Seq
Sample: SRS12891949
BioProject: PRJNA834991
BioSample: SAMN28088451
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: soma
treatment: MG132 10 uM 7H
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078901 34313382 2573503650 926.3 211122DIV17SomaMG132_S10_R1_001.fastq.gz, SRR19078901, SRR19078901.li… SRA
SRX15148782 SRP373580 RNA-Seq SINGLE
GSM6103843: MG132 neurites rep3; Mus musculus; RNA-Seq
Sample: SRS12891950
BioProject: PRJNA834991
BioSample: SAMN28088450
Platform: ILLUMINA
Instrument: NextSeq 500
Organism: Mus musculus
Sample attributes
source_name: Hippocampal neurons
tissue: Hippocampal neurons
strain: C57BL/6
culture: DIV17/18 primary neurons
cell type: neurites
treatment: MG132 10 uM 7H
geo_loc_name: missing
collection_date: missing
Original files (1)
Hippocampal neurons
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR19078900 20930957 1569821775 569.32 211122DIV17DendMG132_S12_R1_001.fastq.gz, SRR19078900, SRR19078900.li… SRA

Linked Publications (2)

Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis.
Nature communications · 2024
Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis.
Nature communications · 2024

Data Files (12)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— 211012DIV18DendCtrl_S3_R1_001.fastq.gz RNA-Seq 320.2 MB link
— 211012DIV18DendMG132_S4_R1_001.fastq.gz RNA-Seq 351.4 MB link
— 211012DIV18SomaCtrl_S1_R1_001.fastq.gz RNA-Seq 476.2 MB link
— 211012DIV18SomaMG132_S2_R1_001.fastq.gz RNA-Seq 385.4 MB link
— 211115DIV17DendCtrl_S7_R1_001.fastq.gz RNA-Seq 496.1 MB link
— 211115DIV17DendMG132_S8_R1_001.fastq.gz RNA-Seq 1.1 GB link
— 211115DIV17SomaCtrl_S5_R1_001.fastq.gz RNA-Seq 338.5 MB link
— 211115DIV17SomaMG132_S6_R1_001.fastq.gz RNA-Seq 229.8 MB link
— 211122DIV17DendCtrl_S11_R1_001.fastq.gz RNA-Seq 368.7 MB link
— 211122DIV17DendMG132_S12_R1_001.fastq.gz RNA-Seq 569.3 MB link
— 211122DIV17SomaCtrl_S9_R1_001.fastq.gz RNA-Seq 405.6 MB link
— 211122DIV17SomaMG132_S10_R1_001.fastq.gz RNA-Seq 926.3 MB link