|
| Status |
Public on Jan 09, 2018 |
| Title |
IFN_0hrs_HIRA_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
IMR90_IFN_0hrs
|
| 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 |
genomic DNA |
| Extraction protocol |
Native ChIP was performed for HIRA and HA-H3.3 as described previously (Rai et al. 2014). Antibodies used for ChIP were: Cocktail of mouse mAbs to HIRA (approximately equimolar mixture of WC15, WC19, WC117, WC 119 (Hall et al. 2001)), HA (Millipore 05904) (for anti-HA-H3.3 ChIP). Mouse mAb to HA tag (Covance, MMS-101R) was used as species/class-matched negative control Abs.
ChIP libraries were prepared for sequencing using standard illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
IMR90 cells at 0hr 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 |
SAMN04254342 |
| SRA |
SRX1426046 |
