|
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 |