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Sample GSM1580662 Query DataSets for GSM1580662
Status Public on Jan 09, 2015
Title RNASeq_IFN
Sample type SRA
Source name HuH7_IFN
Organism Homo sapiens
Characteristics cell line: HuH7
cell type: Human liver (hepato cellular carcinoma) cells
treated with: 10000 units/ml of IFN
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 treated with IFN
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
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
BioSample SAMN03278401
SRA SRX834384

Supplementary file Size Download File type/resource
GSM1580662_IFN.txt.gz 2.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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