|
Status |
Public on Apr 21, 2021 |
Title |
TNFα_mouse_rep4 [mR10_TNF] |
Sample type |
SRA |
|
|
Source name |
TNFα_mouse
|
Organism |
Mus musculus |
Characteristics |
tissue: brain; cortex cell type: Astrocytes treatment: TNFα
|
Treatment protocol |
All treatments were proceeded on 3DIV in serum-free medium. Astrocytes were treated by TNFα for 48hr, by Poly I:C for 72hr, or by hypoxia for 72hr.
|
Growth protocol |
Except that serum selected astrocyte samples were cultured in serum medium, other cultured samples were cultured in defined serum-free medium.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using miRNeasy Mini Kit (Qiagen, 217004) under the protocols of the manufacturer We used the Ovation RNA-seq system V2 (Nugen 7102) to perform first and second-strand cDNA synthesis. We then used the Next Ultra RNA-seq library prep kit for Illumina (NEB E7530) and NEBNext® multiplex oligos for Illumina (NEB E7710 E7500 E7730) to perform end repair, adaptor ligation, and 9-10 cycles of PCR enrichment according to manufacturer’s instructions.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
TNFα_mouse_mR10_BC4
|
Data processing |
FASTQ files were mapped using STAR, then use the output BAM files do HTSEQ or Rsubread to generate count files. We calculated RPKM by running EdgeR-Limma-Voom in R. Genome_build: GRCm38 and GRCh38 Supplementary_files_format_and_content: excel spreadsheet includes RPKM values for each sample.
|
|
|
Submission date |
Apr 01, 2020 |
Last update date |
Apr 21, 2021 |
Contact name |
Jiwen Li |
E-mail(s) |
ljwen@ucla.edu
|
Organization name |
UCLA
|
Street address |
635 Charles E. Young Dr. S.
|
City |
Los Angeles |
ZIP/Postal code |
90095 |
Country |
USA |
|
|
Platform ID |
GPL21103 |
Series (1) |
GSE147870 |
Conservation and divergence of vulnerability and responses to stressors between human and mouse astrocytes |
|
Relations |
BioSample |
SAMN14517164 |
SRA |
SRX8041837 |