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Sample GSM3196008 Query DataSets for GSM3196008
Status Public on Dec 27, 2018
Title Control DRIP-seq 2
Sample type SRA
 
Source name U2OS cells
Organism Homo sapiens
Characteristics tissue: bone
disease: osteosarcoma
antibody: S9.6
Growth protocol U2OS cells were grown in Dulbecco's modified Eagle's medium (DMEM, Carlo Erba Reagents) supplemented with 10% fetal bovine serum (FBS, Carlo Erba Reagents) and 2 mM L-glutamine (Carlo Erba Reagents). Cell lines were maintained by trypsinization and splitting 2-3 times a week, and incubated at 37°C in 5% CO2.
Extracted molecule genomic DNA
Extraction protocol gDNA was extracted from lysated cells, digested using a restriction enzyme cocktail , incubated with S9.6 antibody and immunoprecipitated
genomic DNA were sonicated. Ligation of Illumina Truseq adapters was performed according to manufacturer’s instructions.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Data processing Adapters trimming performed with Trimmomatic version 0.35
Reads mapping on human genome (hg19) performed with BWA version 0.7.12 with parameters -n 2 -t 8
Reads filtering by Merged Consensus blacklist fron ENCODE (ftp://encodeftp.cse.ucsc.edu/users/akundaje/rawdata/blacklists/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed.gz) and duplicates removal with Samtools version 1.3.1
Peak calling performed with MACS2 version 2.1.1.20160309 with parameters -q 0.05 -m 5 50 -g hs -f BAMPE
Genome_build: hg19
Supplementary_files_format_and_content: Bed files produced by macs2
 
Submission date Jun 18, 2018
Last update date Dec 27, 2018
Contact name Giovanni Capranico
E-mail(s) giovanni.capranico@unibo.it
Organization name University of Bologna
Department FABIT
Lab Capranico
Street address Via Selmi 3
City Bologna
State/province BO
ZIP/Postal code 40127
Country Italy
 
Platform ID GPL20301
Series (1)
GSE115957 DNA damage and genome instability by G-quadruplex ligands are mediated by R-loops in human cancer cells
Relations
BioSample SAMN09443957
SRA SRX4231164

Supplementary file Size Download File type/resource
GSM3196008_CT.filtered.bed.gz 1.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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