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Title: Extrachromosomal DNA (microDNA) in Human, Mouse and Chicken      
availability:
available
aggregation:
instance of dataset
privacy:
not applicable
refinement:
curated
dateReleased:
05-22-2015
ID:
E-GEOD-68644
description:
MicroDNAs are <400-base long extrachromosomal circles found in mammalian cells. Tens of thousands of microDNAs were found in all tissue types, including sperm. MicroDNAs arose preferentially from areas with high gene density, high GC content, high exon density, promoters with activating chromatin modifications and in sperm from the 5'UTR of full-length LINE-1 elements, but were depleted from lamin-associated heterochromatin. Furthermore, analysis of microDNAs from a set of human cancer cell lines revealed lineage-specific patterns of microDNA origins. A survey of microDNAs from chicken cell lines defective in various DNA repair proteins revealed that homologous recombination repair and non-homologous end joining repair pathways are not required for microDNA production. A deletion of the MSH3 protein, involved in DNA mismatch repair, resulted in a significant decrease in microDNA abundance specifically from non-CpG areas of the genome. Thus microDNAs arise as part of normal cellular physiology, either from DNA breaks associated with RNA metabolism or from replication slippage followed by mismatch repair. Circular DNA profiling by high throughput sequencing. Five human, ten mouse and nine chicken samples are analyzed
keywords:
DNA-seq
format:
HTML
storedIn:
Array Express
qualifier:
not compressed
accessType:
landing page
authorization:
none
authentication:
none
primary:
true
accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-68644
format:
JSON
storedIn:
OmicsDI
qualifier:
not compressed
accessType:
download
authorization:
none
authentication:
none
primary:
false
accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-68644.json
format:
XML
storedIn:
OmicsDI
qualifier:
not compressed
accessType:
download
authorization:
none
authentication:
none
primary:
false
accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-68644.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/

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