|
| Status |
Public on Jul 29, 2011 |
| Title |
K562-Preimmune |
| Sample type |
SRA |
| |
|
| Source name |
Chromatin IP with preimmune serum (control for PRAME ChIP)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
antibody: preimmune serum (preV27)
|
| Growth protocol |
K562 cells were cultured in standard conditions with RPMI medium with 10% FBS and antibiotics
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in 1% formaldehyde for 15 minutes, chromatin extracted and sheared using a Bioruptor (Diagenode), immunoprecipitated using the antibodies indicated, purified and sequenced using Illumina Genome Analyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP with preimmune serum (control for PRAME ChIP)
|
| Data processing |
Reads (35 bp) were aligned to the human reference genome HG18 with eland and non-uniquely mappable reads were discarded. The number of Preimmune ChIP-seq reads was normalized to the slightly lower number of PRAME ChIP-seq reads. ChIP-seq reads were directionally extended to the length of the fragments used for sequencing, the number of overlapping sequence reads was determined for each base pair in the genome, averaged over a 10 bp window for visualization in the UCSC genome browser (Wiggle processed file). Peaks were called using MACS. Normalized expression values (NE) for RefSeq genes were computed from RNA-seq data with the Genomatix Region Miner tools.
|
| |
|
| Submission date |
Jan 04, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
H.G. Stunnenberg |
| E-mail(s) |
[email protected]
|
| Phone |
+31-24-3610520
|
| Organization name |
Radboud University
|
| Department |
Department of Molecular Biology (274)
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE26439 |
The tumor antigen PRAME is a substrate recognition subunit of a Cul2-based ubiquitin ligase and is associated with active NFY promoters |
|
| Relations |
| SRA |
SRX037416 |
| BioSample |
SAMN00189607 |
