NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM468212 Query DataSets for GSM468212
Status Public on Dec 17, 2009
Title RAR_ChIPseq_UPR9_5hrZinc_JM33
Sample type SRA
 
Source name UPR9 cells
Organism Homo sapiens
Characteristics agent: 5 hours zinc
antibody: RAR
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 RAR _A704
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 SRX014782
BioSample SAMN00006885
Named Annotation GSM468212_RARa_ChIPseq_UPR9_5hrZinc_JM33.wig.gz

Supplementary file Size Download File type/resource
GSM468212_RARa_ChIPseq_UPR9_5hrZinc_JM33.bed.gz 50.0 Mb (ftp)(http) BED
GSM468212_RARa_ChIPseq_UPR9_5hrZinc_JM33.wig.gz 16.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap