|
| Status |
Public on Mar 30, 2024 |
| Title |
primary rat astrocytes + LPS 4 |
| 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
|
| |
|
| 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 |
SAMN40558077 |
| SRA |
SRX24005150 |
