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| Status |
Public on Aug 29, 2012 |
| Title |
Chromatin accessibility, p300 and histone acetylation define PML-RARalpha- and AML1-ETO-binding sites |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Chromatin accessibility is a key determinant of cell-type-specific gene expression. Here, we have investigated the chromatin architecture of different acute myeloid leukemia (AML) cells and the changes in accessibility when NB4 (APL) cells undergo the process of differentiation.
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| Overall design |
For nuclease-accessible site sequencing (NA-seq; Gargiulo et al. 2009), chromatin-accessible libraries were generated in different AML leukemic cells by using restriction enzymes NlaIII and HpaII. In the case of NB4 cells, accessibility was mapped both before and after treatment with all-trans retinoic acid (ATRA) for 48hr. Differences were observed between the two conditions, and chromatin accessibility was correlated with underlying epigenetic modifications. For validation purposes, NA-seq libraries (using the NlaIII enzyme) were generated in APL and AML M1 patient's blasts. All of the ChIP-seq (Martens et al. 2010) studies were performed in leukemic NB4 and SKNO-1 cells.
Supplementary file 'GSE30254_All_accessibleregions_ATRA_NB4_fseq.wig' includes data for Samples GSM749512, GSM749513, GSM749516, and GSM749517.
Supplementary file 'GSE30254_All_accessibleregions_untreated_NB4_fseq.wig' includes data for Samples GSM749510, GSM749511, GSM749514, and GSM749515.
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| Contributor(s) |
Stunnenberg HG, Martens JH, Saeed S, Logie C, Francoijs K, Frigè GM, Romanenghi M, Nielsen F, Raats L, Shahhoseini M, Huynen M, Altucci L, Minnuci S |
| Citation(s) |
22923494 |
| Submission date |
Jun 27, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
H.G. Stunnenberg |
| E-mail(s) |
h.stunnenberg@ncmls.ru.nl
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| Phone |
+31-24-3610520
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| Organization name |
Radboud University
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| Department |
Department of Molecular Biology (274)
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| Street address |
Geert Grooteplein 28
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| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
USA |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (25)
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| Relations |
| SRA |
SRP007344 |
| BioProject |
PRJNA143747 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE30254_All_accessibleregions_ATRA_NB4_fseq.wig.gz |
46.7 Mb |
(ftp)(http) |
WIG |
| GSE30254_All_accessibleregions_untreated_NB4_fseq.wig.gz |
46.6 Mb |
(ftp)(http) |
WIG |
| GSE30254_RAW.tar |
2.3 Gb |
(http)(custom) |
TAR (of BED, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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