|
| Status |
Public on Jun 03, 2021 |
| Title |
IFNb_TIC_1 |
| Sample type |
SRA |
| |
|
| Source name |
P5 rat brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
stimulation: IFNb (1000 U/ml)+TIC
cell type: Primary rat astrocytes
|
| Treatment protocol |
Primary immunopanned astrocytes were treated with IFNg (3 ng/ml), IFNb (1000 U/ml), TNFa (30 ng/ml)+IL1a (3 ng/ml) +C1q (40 ng/ml) or combincations thereof for 24h, RNA collected and sequenced on a NovaSeq6000
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Agilent Absolutely Total RNA Purification Kit
cDNA was generated using the SMART-seq HT kit and libraries were generated using the Nextera XT kit (Takara Bio).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequences, aligned to the mm10 reference genome using HISAT2 followed by transcript assembly and quantification using StringTie
Differential gene expression was assessed using DESeq2. Expression values are given as FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: processed file includes FPKM, padj (DESeq2) and log 2 fold changes
|
| |
|
| Submission date |
Jan 19, 2021 |
| Last update date |
Jun 03, 2021 |
| Contact name |
Philip Hasel |
| E-mail(s) |
philip.hasel@nyulangone.org
|
| Organization name |
NYU Langone Medical Centre
|
| Street address |
435 E 30th St
|
| City |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (2) |
| GSE148612 |
Neuroinflammatory astrocyte subtypes in the mouse brain |
| GSE165069 |
Neuroinflammatory astrocyte subtypes in the mouse brain [bulk RNA-seq, Interferon_in_vitro] |
|
| Relations |
| BioSample |
SAMN17379514 |
| SRA |
SRX9894459 |
