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| Status |
Public on Sep 08, 2016 |
| Title |
ChIP-seq-based analysis of i) K27me3 promoter coverage and ii) enhancer elements in neuroblastoma cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
To investigate whether a set of differentially methylated/expressed genes, identified in neuroblastomas of differential outcome, co-localizes with K27me3 marks or enhancer elements, we performed H3K4me3, H3K4me1, H3K27ac and H3K27me3 ChIP seq in neuroblastoma cell lines.
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| Overall design |
Enhancers were defined in neuroblastoma cell lines as overlapping H3K4me1 and H3K27ac peaks with a minimal distance of 2 kb to the closest H3K4me3 peak, a criterion imposed to rule out selection of (unannotated) promoters. Promoter-near K27me3 coverage was also analyzed in neuroblastoma cell lines. The effect of MYCN on K27me3 occupancy was investigated upon modulation of MYCN levels.
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| Contributor(s) |
Henrich KO, Bender S, Saadati M, Gartlgruber M, Shao C, Herrmann C, Parzonka M, Dreidax D, Fischer M, Duffy DJ, Schmezer P, Plass C, Höfer T, Benner A, Pfister SM, Westermann F |
| Citation(s) |
27635046 |
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| Submission date |
Apr 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Chunxuan Shao |
| E-mail(s) |
c.shao@Dkfz-Heidelberg.de
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| Organization name |
German Cancer Research Center
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| Street address |
Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (19)
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| Relations |
| BioProject |
PRJNA318261 |
| SRA |
SRP073195 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE80197_RAW.tar |
653.7 Mb |
(http)(custom) |
TAR (of TDF) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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