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Sample GSM7916079 Query DataSets for GSM7916079
Status Public on Nov 27, 2023
Title Astrocytes, PGC-1a2 adenovirus infected, rep3
Sample type SRA
 
Source name mouse primary astrocyte cells
Organism Mus musculus
Characteristics strain: CD-1
cell line: mouse primary astrocyte cells
cell type: astrocytes
genotype: wild-type
treatment: Adenovirus infection
condition: Ad_PGC1alpha2
Treatment protocol Cells were transduced with adenovirus expressing GFP, used as control, or each different PGC-1α isoform at a multiplicity of infection (MOI) of 100, for 24 h.
Growth protocol Primary cultures of mouse astrocytes were prepared from 1 to 3-day-old CD-1 pups. Cells were maintained at 37°C in a humidified atmosphere of 5% CO2. The medium was firstly changed after 7 days, and then every 3 days, until cultures were confluent at 10 to 13 days in vitro (DIV).
Extracted molecule polyA RNA
Extraction protocol Cells were lysed and RNA was extracted using Trizol reagent
Samples were purified by poly-A enrichment before library creation using Illumina TruSeq mRNA.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR 2.7.3a with extra arguments --outFilterMismatchNmax 33 --alignEndsType Local --alignSJoverhangMin 8 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --seedSearchStartLmax 12
Reads aligning to gene exons were counted using featureCounts v2.0.3 program from Subread package, summarized at gene level.
Differential gene expression at FDR level 0.05 was obtained using DESeq2 R package, genes with total raw counts less then 10 across all samples were excluded from analysis
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw read counts for all samples
Supplementary files format and content: tab-delimited text file includes differetial gene expression analysis output from DESeq2
 
Submission date Nov 22, 2023
Last update date Nov 27, 2023
Contact name Igor Cervenka
E-mail(s) igor.cervenka@ki.se
Organization name Karolinska Institutet
Department Physiology and Pharmacology
Lab MCEP
Street address Solnavägen 9
City Solna
ZIP/Postal code 17165
Country Sweden
 
Platform ID GPL17021
Series (1)
GSE248504 Sustained PGC-1α2 or PGC-1α3 expression induces astrocyte dysfunction and degeneration.
Relations
BioSample SAMN38375157
SRA SRX22617918

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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