|
| Status |
Public on May 06, 2020 |
| Title |
TOV21G-8h-2 |
| Sample type |
SRA |
| |
|
| Source name |
TOV21G-8h-2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: TOV21G
treatment: IFNg 8h Rep2
genotype/variation: ARID1A mut
|
| Treatment protocol |
WT and KO cells were treated with interferon for indicated time points.
|
| Growth protocol |
OVCA429 cells was cultured as previously reported.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen).
The Illumina Ribo-Zero Gold rRNA Removal Kit (Cat# MRZG126) was used for RNA-sequencing library preparation for RNA-sequencing. Sequencing was performed by paired-end 50-mer sequencing in replicates at the University of Michigan sequencing core facility with HiSeq 4000 (Illumina). The sequenced raw reads of each sample were aligned to the human reference genome GRCh 38 .
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The sequenced raw reads of each sample were aligned to the human reference genome GRCh 38 using STAR, HISAT2 .
The transcriptome was self-merged to allow processing with StringTie
Different conditions were compared using ballgown R package, Limmar.
Other methods also were used to validate it.
Genome_build: GRCh 38
Supplementary_files_format_and_content: Excel File with gene expression values
|
| |
|
| Submission date |
May 29, 2019 |
| Last update date |
May 06, 2020 |
| Contact name |
Jing Li |
| E-mail(s) |
jingdsli@umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Surgery
|
| Street address |
500 S State St,
|
| City |
Ann Arbor, |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE131916 |
RNA-seq in ARID1A WT, KO OVCA429 Cells after IFNγ treatment |
| GSE131918 |
ARID1A gene status shapes cancer immune phenotype and affects cancer immunotherapy |
|
| Relations |
| BioSample |
SAMN11883843 |
| SRA |
SRX5924979 |
