|
Status |
Public on Mar 30, 2024 |
Title |
primary rat astrocytes + LPS 3 |
Sample type |
SRA |
|
|
Source name |
cortical
|
Organism |
Rattus norvegicus |
Characteristics |
tissue: cortical age: Postnatal day 1 cell type: astrocytes strain: Wistar treatment: LPS (100ng/ml)
|
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
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|
|
Submission date |
Mar 20, 2024 |
Last update date |
Mar 30, 2024 |
Contact name |
Joel Gruchot |
E-mail(s) |
joel.gruchot@hhu.de
|
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 |
|
Relations |
BioSample |
SAMN40558079 |
SRA |
SRX24005148 |