|
| Status |
Public on Jun 18, 2013 |
| Title |
YB-1 ChIP |
| Sample type |
SRA |
| |
|
| Source name |
Human Embryonic Kidney cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
passages: p20
chip antibody: anti-HA ChIP-grade (ab9110), Abcam
chip antibody catalog #: Abcam
chip antibody manufacturer: ab9110
|
| 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 |
SAMN02183443 |
| SRA |
SRX288287 |
