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Status |
Public on Nov 27, 2023 |
Title |
Astrocytes, PGC-1a2 adenovirus infected, rep3 |
Sample type |
SRA |
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Source name |
mouse primary astrocyte cells
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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
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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
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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 |