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Title: ChIP-chip analysis to determine GLI2 binding sites      
availability:
available
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instance of dataset
privacy:
not applicable
refinement:
curated
dateReleased:
05-03-2014
ID:
E-GEOD-39255
description:
Chromatin immunoprecipitation with anti-GLI2 antibody was conducted in human pulomonary microvascular endothelial cells (HPMECs) to determine GLI2 binding sites upstream of FOXF1. An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development. ChIP-chip HPMECs transfected to overxpress GLI2; 2 biological replicates
keywords:
ChIP-chip by tiling array
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storedIn:
Array Express
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primary:
true
accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39255
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JSON
storedIn:
OmicsDI
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accessType:
download
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false
accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-39255.json
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XML
storedIn:
OmicsDI
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not compressed
accessType:
download
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none
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primary:
false
accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-39255.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/