|
Status |
Public on Jun 18, 2013 |
Title |
input DNA |
Sample type |
SRA |
|
|
Source name |
Human Embryonic Kidney cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: HEK293 passages: p20 chip antibody: none
|
Growth protocol |
HEK293 cells were cultivated in DMEM (PAA Laboratories) supplemented with 10% FCS (Invitrogen) and antibiotics (penicillin (100 U/ml) and streptomycin (100 μg/ml))
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Nuclei were disrupted using LB3 buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDeoxycholate, 0.5% N-lauroylsarcosine) Illumina TruSeq DNA Sample Preparation Kit v2 (Illumina, San Diego)
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
All samples were sequenced with 50 basepair single-end reads and multiplexing using Illumina’s third-read barcoding scheme
|
Data processing |
Initial data processing and quality was performed using the CASAVA (v 1.8.2 Illumina) and FastQC Sequencing reads were trimmed by clipping regions with low base-calling quality or adapter contamination Resulting quality-filtered reads were aligned to the hg19/GRCh37 assembly of the human genome using Bowtie UCSC Genome Browser WIG/bigWig tracks and peak calls were established using the MACS software with default parameters Genome_build: hg19 Supplementary_files_format_and_content: peaks txt, wig (peaks)
|
|
|
Submission date |
May 30, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Gerhard Duernberger |
Organization name |
CeMM
|
Street address |
Lazarettgasse 14, AKH BT 25.3
|
City |
Vienna |
ZIP/Postal code |
1090 |
Country |
Austria |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE47539 |
Experimental characterization of the human non-sequence-specific nucleic acid interactome |
|
Relations |
BioSample |
SAMN02183444 |
SRA |
SRX288288 |