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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

Comparison of CNV in 6 ostosarcoma cell lines

Project description:We evaluated 6 established ostesarcoma cell lines. Copy Number Variation and loss-of-heterozygosity status were explored to look for similar patterns across cell lines

2023-11-22 | GSE240546 | GEO

Gene Expression Networks in the Drosophila Genetic Reference Panel

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.

2020-02-28 | GSE117850 | GEO

Human Variation Panel: Gene Expression and Genotype

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

2010-09-24 | E-GEOD-24277 | biostudies-arrayexpress

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

2010-03-01 | E-GEOD-15096 | biostudies-arrayexpress

Human Variation Panel: Gene Expression and Genotype

Project description:Human Variation Panel: Gene Expression and Genotype

| PRJNA129983 | ENA

Identification of transcripts harboring premature termination codons by NMD inhibition in a panel of CCRCC cell lines

Project description:Identification of transcripts harbouring premature termination codons by NMD inhibition (GINI method) in a panel of clear cell renal cell carcinoma cell lines. Sporadic clear cell renal cell carcinoma (cRCC) is genetically characterized by the recurrent loss of chromosome 3p, with a hotspot for copy number loss in the 3p21 region. In this study, we applied a method called Gene Identification by Nonsense Mediated mRNA decay Inhibition (GINI) on a panel of 10 cRCC cell lines with 3p21 copy number loss to identify biallelic inactivated genes located at 3p21. This analysis revealed inactivation of the histone methyltransferase gene SETD2, located on 3p21.31, as a common event in cRCC cells. SETD2 is nonredundantly responsible for trimethylation of the histone mark H3K36. Consistent with this function, we observed loss or decrease of H3K36me3 in 7 out of 10 cRCC cell lines. Identification of missense mutations in 2 of 10 primary cRCC tumor samples further supported the involvement of loss of SETD2 function in the development of cRCC tumors.

2010-02-25 | GSE20491 | GEO

Seeking novel mammalian genes using transcript profiling and genotyping of a human radiation hybrid panel

Project description:Using a human-hamster radiation hybrid panel (G3), we have mapped loci regulating gene expression due to copy number increase.

2012-04-09 | GSE19003 | GEO

Copy number variation data in malignant mouse mammary cell lines

Project description:Many preclinical therapy studies have focused on a small number of well-described mouse allograft or human xenograft models that poorly represent the heterogeneity of human disease. Here we have assembled a panel of mouse mammary cell lines derived from spontaneously-arising mouse mammary tumors or from mammary tumors arising in genetically engineered mouse models. We used the Affymetrix Mouse Diversity Genotyping Array to address DNA copy number variation in the genomes of the cell lines of this panel. The resulting information about regions of amplification and deletion should help inform biological analyses as well as provide a reference for cell line authentication/identification.

2016-06-15 | GSE69902 | GEO

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