|
| 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 |
