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High resolution genome wide DNA analysis on a large panel of Human Embryonic stem cell lines

ABSTRACT: High resolution genome wide DNA analysis on a large panel of Human Embryonic stem cell lines reveals loss of heterozygosity and copy number variation changes associated with culture and affecting gene expression This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE15097 | GEO | 2010/03/01

SECONDARY ACCESSION(S): PRJNA114881

REPOSITORIES: GEO

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High resolution genome wide DNA analysis on a large panel of Human Embryonic stem cell lines

Project description:High resolution genome wide DNA analysis on a large panel of Human Embryonic stem cell lines reveals loss of heterozygosity and copy number variation changes associated with culture and affecting gene expression This SuperSeries is composed of the following subset Series: GSE15095: Exon arrays for human embryonic stem cells GSE15096: Affymetrix SNP 6.0 array data for human embryonic stem cell lines

2010-02-28 | E-GEOD-15097 | biostudies-arrayexpress

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Project description:A major challenge of modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal phenotypes through networks of intermediate molecular phenotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and mapped expression quantitative trait loci for annotated genes, novel transcribed regions (most of which are long noncoding RNAs), transposable elements and microbial species. We identified host variants affecting expression of transposable elements independent of copy number and microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination and are associated with transposable element expression. This study uncovers novel genetic features that regulate natural genetic variation of gene expression and generates testable hypotheses for future functional analyses.

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Project description:This SuperSeries is composed of the following subset Series: GSE23120: Basal gene expression data from Human Variation Panel GSE24245: Genome-wide SNP array data from Human Variation Panel by Illumina 510S GSE24260: Genome-wide SNP array data from Human Variation Panel by Illumina 550K GSE24274: Genome-wide SNP array data from Human Variation Panel by Illumina 650K Refer to individual Series

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Affymetrix SNP 6.0 array data for human embryonic stem cell lines

Project description:Pluripotent human embryonic stem cells are studied for potential applications in regenerative cell replacement therapies because of their untransformed nature and unique capacity to self-renew and differentiate. However it is known that adaptation of hESCs occurs on prolonged culture and may be associated with the acquisition of chromosome abnormalities. We report a high resolution DNA SNP 6.0 array analysis showing copy number variation in 17 different hESC lines maintained in different laboratories. Several of the changes were culture induced and changed the expression levels of affected genes. Loss of heterozygosity (LOH) of chromosome 16q was detected in one line, in addition to several smaller LOH regions. Importantly, hESCs were found to contain several CNVs less than 3 Mb in size which is below the detection limit of conventional karyotyping.

2010-03-01 | GSE15096 | GEO

Affymetrix SNP 6.0 array data for human embryonic stem cell lines

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Human Variation Panel: Gene Expression and Genotype

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