|
| Status |
Public on Feb 28, 2018 |
| Title |
NG-18_siIRF9-IFN-TNF |
| Sample type |
SRA |
| |
|
| Source name |
U3A cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line : Human U3A cell line. The STAT1-deficient U3A cells were obtained by mutagenesis of 2ftGH cells originally derived from HT1080 fibrosarcoma cells (McKendry R, et al.Proc Natl Acad Sci U S A. 1991;88(24):11455-9)
cell type: epithelial
tissue: Connective tissue
disease: Fibrosarcoma
gender: Male
age: 35
ethnicity: Caucasian
|
| Treatment protocol |
Transfection: IRF9-targeting siRNA using Oligofectamine
Stimulation : IFNb (1000U/ml) +TNFa (10ng/ml)
|
| Growth protocol |
Cells were grown in DMEM medium supplemented with 10% Heat-Inactivated-FBS or Heat-Inactivated-Fetal Clone III (HI-FCl) and 1% L-glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNASeq stranded
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37
Supplementary_files_format_and_content: comma-delimited text files include Raw reads and RPKM values for each Sample ...
|
| |
|
| Submission date |
Feb 27, 2018 |
| Last update date |
Jul 03, 2019 |
| Contact name |
Nathalie Grandvaux |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Montreal
|
| Street address |
2900, boul. Édouard-Montpetit
|
| City |
Montreal |
| ZIP/Postal code |
H3T1J4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE111195 |
Genome wide characterization of a STAT1-independent antiviral and immunoregulatory transcriptional program induced by IFNβ and TNFα reveals non-canonical STAT2 and IRF9 pathways |
|
| Relations |
| BioSample |
SAMN08617235 |
| SRA |
SRX3747436 |
