|
| Status |
Public on Jan 09, 2015 |
| Title |
RNASeq_Huh7 |
| Sample type |
SRA |
| |
|
| Source name |
HuH7_control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HuH7
cell type: Human liver (hepato cellular carcinoma) cells
treated with: none (control)
time point: 3 days post-treatment
|
| Treatment protocol |
HuH7 cells were treated with 10000 units/ml of IFN a2 and RNA was isolated 3 days post-treatment
|
| Growth protocol |
HuH7 cells were incubated at 37 degress in 5% CO2 environment with DMEM media plus antibiotics and 10% FCS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with TRIZOL (SIGMA)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Gene expression analysis of HuH7 cells
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
The processing of reads included elimination of contaminant adaptar substrings with Scythe and quality-based trimming using Sickle. The alignment of reads to the human genome (hg19) was performed using Tophat2 mapper.
The transcript assembly and quantification using FPKM of transcripts was carried out using Cufflinks2.
Annotation of the gene locus obtained was performed using Cuffmerge with Gencode v19 as reference.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample using cufflinks and GENCODE v19
|
| |
|
| Submission date |
Jan 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Victor Segura |
| E-mail(s) |
vsegura@unav.es
|
| Organization name |
FIMA
|
| Department |
Unit of Proteomics, Genomics and Bioinformatics
|
| Street address |
Avda. Pío XII, 55
|
| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE64795 |
Type I interferon regulates the expression of long non-coding RNAs [RNA-seq] |
| GSE64796 |
Type I interferon regulates the expression of long non-coding RNAs |
|
| Relations |
| BioSample |
SAMN03278400 |
| SRA |
SRX834383 |
