|
| Status |
Public on Sep 01, 2016 |
| Title |
ChIP_goatIgG_U2OS |
| Sample type |
SRA |
| |
|
| Source name |
U2OS
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
cell type: osteosarcoma
chip antibody: normal goat IgG (sc-2028, Santa Cruz Biotechnology)
|
| Growth protocol |
cells were cultured in media supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.
Libraries were constructed according to Illuminas standard protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing reads were mapped to the human genome (NCBI36)
peaks called with koli as described before
Genome_build: hg18
Supplementary_files_format_and_content: Chromosome, peak start and peak end refers to to genome assembly NCBI36; Peak summit defined as the point of maximum height that is closest to the center of the peak; Peak height the maximum number of overlapping sequences; Fold change calculated from the areas of the peaks in the ChIP sample vs. IgG sample; p-value probability of observing the difference between the sequence counts in the ChIP sample and IgG control by chance estimated using Winflat program
|
| |
|
| Submission date |
May 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Maria Sokolova |
| E-mail(s) |
maria.fulop@helsinki.fi
|
| Organization name |
University of Helsinki
|
| Department |
Institute of Biotechnology
|
| Lab |
Nuclear Actin Lab
|
| Street address |
Viikinkaari 5
|
| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE69147 |
Histone genes transcription regulators binding in human cancer (U2OS) and normal (hTERT-RPE1) cells |
| GSE69149 |
Histone gene regulation in normal and tumor cells |
|
| Relations |
| BioSample |
SAMN03704247 |
| SRA |
SRX1036444 |
