|
| Status |
Public on Apr 21, 2021 |
| Title |
TNFα_control_mouse_rep2 [mR6_Ctrl] |
| Sample type |
SRA |
| |
|
| Source name |
TNFα_control_mouse
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain; cortex
cell type: Astrocytes
treatment: TNFα_control
|
| 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_control_mouse_mR6_BC3
|
| 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 |
SAMN14517172 |
| SRA |
SRX8041829 |
