|
| Status |
Public on Sep 17, 2010 |
| Title |
BAP18-GFP_HeLa rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Human cervical carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa Kyoto cell line
sample type: Antibody GFP Abcam (ab290-050); HeLa cells stably transfected with BAP18-GFP BAC
antibody: anti-GFP
antibody manufacturer: Abcam
antibody catalog #: ab290-050
transfection: BAP18-GFP BAC
|
| Growth protocol |
Transfected HeLa Kyoto cells were FACS sorted (Epics Altra flowcytometer, Beckman Coulter) for GFP positive cells, and cultured for 3-4 passages in DMEM with 10% FCS under 500 µg/ml G418 selection at 37˚C before usage for the ChIP and ChIP-Seq experiments. Generation of the BACs with GFP-fusion constructs within the endogenous genomic context of the target gene, and transfections of HeLa cells, were performed according to Poser et al (2008).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Stable Transfections with GFP-fusion constructs within the endogenous genomic context of the target gene
ChIP experiments were performed using 3.3x10^6 cells per ChIP according to standard protocols (Denissov et al, 2007), with two minor modifications. Crosslinking of the cells was performed on the culture plates for 20 minutes, while ChIP’ed DNA was purified by Qiaquick PCR purification Kit (Qiagen cat. no. 28106).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP against GFP
|
| Data processing |
Reads (36 bp) were aligned to the human (Homo Sapiens) reference genome. Sequences were aligned to the human HG18 reference genome using the Illumina Analysis Pipeline allowing one mismatch. Unless specified otherwise, only the tags uniquely aligning to the genome were considered for further analysis. The 36 bp sequence reads were directionally extended to 300 bp, corresponding to the length of the original fragments used for sequencing. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All ChIP-Seq sequence analyses were conducted based on the Human NCBI Built 36.1 genome assembly (HG18) accessed from the Ensembl (release 54; May 2009) or the UCSC (assembly March 2006) Genome Browsers.
|
| |
|
| Submission date |
Jul 13, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Hendrik Marks |
| E-mail(s) |
h.marks@ncmls.ru.nl
|
| Organization name |
Radboud University Nijmegen, RIMLS
|
| Department |
Molecular Biology
|
| Street address |
Geert Grooteplein 26/28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE20303 |
ChIP-Seq sequencing of novel interactors of H3K4me3, H3K36me3 and H3K9me3 |
|
| Relations |
| SRA |
SRX023651 |
| BioSample |
SAMN00017111 |
