|
| Status |
Public on Dec 17, 2009 |
| Title |
RXR_ChIP-seq_APL74_noATRA_JM25 |
| Sample type |
SRA |
| |
|
| Source name |
APL cells _pz74
|
| Organism |
Homo sapiens |
| Characteristics |
agent: none
antibody: RXR
|
| Treatment protocol |
Leukemic cells NB4, MR4, APL were treated with ATRA for 24 or 48 hours, UPR9 cells with zinc for 5 hours.
|
| Growth protocol |
Leukemic cells were cultured in normal cell culture containing 10% serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor Diagenode, immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Antibody RXR _sc774
|
| Data processing |
Reads (32 bp) were aligned to the Human (UCSC 36.1 (hg18)) reference genome. RNAPII tracks for the different treatment periods (0, 24 and 48 hours) were equalized for the total number of mapped tags by random removal of sequenced tags. For PML, RAR and RXR, enriched intervals were identified using MACs. For RNAPII number of tags within ENSEMBLE genes (from +500 from TSS to end of gene) were counted and gene regulation was expressed as ratio of tags after 24 or 48 hours treatment divided by the tags in the same gene region before treatment.
|
| |
|
| Submission date |
Nov 04, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
H.G. Stunnenberg |
| E-mail(s) |
h.stunnenberg@ncmls.ru.nl
|
| 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 |
GPL9052 |
| Series (1) |
| GSE18886 |
PML-RARa/RXR alters the epigenetic landscape in Acute Promyelocytic Leukemia |
|
| Relations |
| SRA |
SRX014774 |
| BioSample |
SAMN00006877 |
| Named Annotation |
GSM468204_RXR_ChIPseq_APL74_noATRA_JM25.wig.gz |
