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Sample GSM8156289 Query DataSets for GSM8156289
Status Public on Mar 30, 2024
Title primary rat astrocytes + H2O 4
Sample type SRA
Source name cortical
Organism Rattus norvegicus
Characteristics tissue: cortical
age: Postnatal day 1
cell type: astrocytes
strain: Wistar
treatment: H2O
Treatment protocol One day after microglial isolation or 3 days after astroglial isolation, cells were stimulated with with 1 µg/ml recombinant HERV-W ENV protein or with 100 ng/ml LPS in glial media (10% FCS, 2 mM L-glutamine, 50 U/ml penicillin/streptomycin in DMEM).
Growth protocol Briefly, dissociated P1 Wister rat cortices were cultured on T-75 cell culture flasks in Dulbecco′s Modified Eagle′s Medium (DMEM) substituted with 10% fetal calf serum (FCS) and 4 mM L-glutamine, 50 U/ml penicillin/streptomycin. After 10 days, flasks were shaken at 180 rpm/min at 37 °C and microglia-containing supernatants were collected after 2 and 24 h. To further purify the primary rat microglia, cells were sorted using MACS against CD11b/c microbeads.
Extracted molecule total RNA
Extraction protocol RNA was harvested using Rneasy mini kit (Qiagen) and 150 ng of total RNA was used for the library construction
RNA libraries for RNA-Seq were prepared according to the manifacturers protocol using the VAHTS™ Universal RNA-Seq Library Prep Kit for Illumina® V6 with mRNA capture module
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq X Plus
Data processing raw data in FASTQ format were adapter- and quality trimmed.
Mapping was performed against the Rattus norvegicus (mRatBN7.2.1110; January 05, 2024) genome sequence using Hisat2 alignment method.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach
Assembly: mRatBN7.2.1110
Supplementary files format and content: raw counts as .txt
Submission date Mar 20, 2024
Last update date Mar 30, 2024
Contact name Joel Gruchot
Organization name Heinrich-Heine-University
Department Neurology
Street address Moorenstraße 5
City Düsseldorf
ZIP/Postal code 40225
Country Germany
Platform ID GPL34316
Series (1)
GSE262029 Molecular dissection of HERV-W dependent microglial- and astroglial cell polarization
BioSample SAMN40558078
SRA SRX24005149

Supplementary file Size Download File type/resource
GSM8156289_AS_6ctrl.txt.gz 93.0 Kb (ftp)(http) TXT
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Raw data are available in SRA

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