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Sample GSM1936746 Query DataSets for GSM1936746
Status Public on Jan 09, 2018
Title ShHIRA_2_IFN_6hrs_Replicate2
Sample type SRA
 
Source name IMR90_shHIRA_2_IFN_6hrs
Organism Homo sapiens
Characteristics cell line: IMR90
Treatment protocol IMR90 cells were treated with 2000U/ml recombinant human IFN-β (PBL-11410-2)
Growth protocol IMR90 cells were cultured in DMEM supplemented with 20% (v/v) FBS, 2 mM L-Glutamine and incubated at 37°C in a humidified 5% CO2 and 3% O2 atmosphere. Cell Growth media were supplemented with 100 U/ml penicillin and 100 ug/ml streptomycin.
Extracted molecule polyA RNA
Extraction protocol Total RNA was prepared using the RNeasy kit (Qiagen catalog no. 74104), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description IMR90 cells with HIRA KD at 6hr IFN treatment
Data processing Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
RNA-seq reads were mapped to hg19 whole genome using tophat 2.0.9 with parameters –solexa-quals, -p 12, --segment-length 18, -M, -G Homo_sapiens.GRCh37.73.gtf
ChIP-seq reads were mapped to hg19 whole genome using bowtie 2.1.0 with parameters -p 12
Aligned reads normalised by library size (number of fragments) and subsequent reads piledup and converted to bigWig format
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base. bigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig.
 
Submission date Nov 10, 2015
Last update date May 15, 2019
Contact name Peter Adams
Organization name University of Glasgow, Beatson Institute for Cancer Research
Street address Switchback Rd, Bearsden
City Glasgow
ZIP/Postal code G61 1BD
Country United Kingdom
 
Platform ID GPL10999
Series (1)
GSE74863 Expression data and HIRA ChIP-seq data from interferon treated IMR90 cells
Relations
BioSample SAMN04254333
SRA SRX1426037

Supplementary file Size Download File type/resource
GSM1936746_shHIRA2.24hrs.rep2.lane5.FPKM.txt.gz 1.9 Mb (ftp)(http) TXT
GSM1936746_shHIRA2.24hrs.rep2.lane5.bigwig 149.7 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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