|
| Status |
Public on Jul 31, 2012 |
| Title |
Input_DNA_seq3 |
| Sample type |
SRA |
| |
|
| Source name |
Suspension HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa, cycling
chip antibody: None
|
| Treatment protocol |
HeLa-S cells were crosslinked for 8â using 1% of formaldehyde, DNA was isolated and sonicated to 100-300 bps using a bioruptor (Bioruptor UCD-200, Diagenode) and 30ââ pulses on and off at maximum power. Sonicated DNA was immunoprecipitated, washed and eluted as described (Shweta 2007). 2-8 x 107 cells were used per antibody.
|
| Growth protocol |
HeLa-S cells were grown in suspension in Joklik's modified Eaglesâs medium (JMEM) with 5% of fetal calf serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
5-10ng of ChIP-DNA were transformed into libraries using ChIP-Seq DNA Sample Prep Kit (Illumina) and sequenced on Illumina Genome Analyzer 2 DNA sequencing instrument. Total input DNA was also sequenced.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
High-throughput sequencing of control input DNA (collected after the crosslinking and sonication steps)
|
| Data processing |
Alignment : The sequenced tags were mapped onto the unmasked genome build hg18 using the fetchGWI software. Only the tags with a unique and perfect match were kept for the analysis
Peak detection : peaks were determined with the sissrs software (www.rajajothi.com/sissrs/). Peaks common to the control input material and the ChIP material, as well as peaks mapping in satellite and micro-satellite repeats and peaks mapping in 18 and 28S rRNA sequences, were eliminated from the analysis.
|
| |
|
| Submission date |
Aug 16, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicolo Riggi |
| Organization name |
CHUV
|
| Department |
Département de Pathologie Expérimentale
|
| Lab |
Institut universitaire de pathologie
|
| Street address |
Bugnon 25
|
| City |
Lausanne |
| State/province |
VD |
| ZIP/Postal code |
1011 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL9115 |
| Series (3) |
| GSE31412 |
Expression changes in HeLa cells treated with siRNA against HCFC1 or control luciferase |
| GSE31417 |
Genome-wide study of HCFC1 binding sites and its associated transcription factors in cycling Human HeLa cells |
| GSE31419 |
The epigenetic cell-cycle regulator HCF-1 is recruited to active CpG island-containing promoters together with the ZNF143, THAP11(Ronin), YY-1 and GABP transcription factors. |
|
| Relations |
| SRA |
SRX092572 |
| BioSample |
SAMN00710517 |
