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Series GSE55407 Query DataSets for GSE55407
Status Public on Feb 27, 2014
Title Classifying leukemia types with chromatin conformation data (ChIP-Seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Background: Although genetic or epigenetic alterations have shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed.
Results: Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data.
Conclusions: Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes.
Overall design Examination of CTCF and RAD21 binding sites in THP-1 cell.
Contributor(s) Rousseau M, Ferraiuolo MA, Crutchley JL, Wang XQ, Miura H, Blanchette M, Dostie J
Citation(s) 24995990
Submission date Feb 26, 2014
Last update date May 15, 2019
Contact name Josée Dostie
Phone 1-514-398-4975
Organization name McGill University
Department Biochemistry
Street address 3655 Promenade Sir-William-Osler
City Montreal
State/province QC
ZIP/Postal code H3G 1Y6
Country Canada
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (3)
GSM1335528 CTCF_ChIP-seq
GSM1335529 RAD21_ChIPseq
GSM1335530 WCE_DNA
This SubSeries is part of SuperSeries:
GSE55408 Classifying leukemia types with chromatin conformation data
BioProject PRJNA239520
SRA SRP038996

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Supplementary file Size Download File type/resource
GSE55407_RAW.tar 135.3 Mb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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