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Exon arrays for human embryonic stem cells

ABSTRACT: Samples were used to study if genomic copy number variation changes detected with SNP 6.0 array would correlate with the expression level changes in human embryonic stem cells These samples were used as a portion of the study evaluating the genomic stability and its effects on human embryonic stem cells in prolonged culture.

ORGANISM(S): Homo sapiens

PROVIDER: GSE15095 | GEO | 2010/03/01

SECONDARY ACCESSION(S): PRJNA123215

REPOSITORIES: GEO

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Exon arrays for human embryonic stem cells

Project description:Samples were used to study if genomic copy number variation changes detected with SNP 6.0 array would correlate with the expression level changes in human embryonic stem cells These samples were used as a portion of the study evaluating the genomic stability and its effects on human embryonic stem cells in prolonged culture. Selected nine human embryonic stem cell samples from different lines having different kind of genomic abnormalities were hybridized to exon arrays.

2010-05-06 | E-GEOD-15095 | biostudies-arrayexpress

SKOV3 cells comparative genomic hybridization

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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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Pancreatic endocrine tumour (PET)_Affymetrix 500K SNP arrays

Project description:To identify genetic alterations involved in the pathogenesis of PETs, we have analysed a total of 32 PET samples (29 tissue specimens and 3 cell lines) using high-resolution single nucleotide polymorphism (SNP) arrays. Keywords: comparative genomic hybridisation

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A missense mutation in TFRC, encoding transferrin receptor 1, causes combined immunodeficiency (Family A)

Project description:Affymetrix 6.0 SNP data for genome-wide linkage scans of a consanguineous Kuwaiti family with a combined immunodeficiency Peripheral blood or saliva were used for patients who had no history of hematopoietic stem cell transplant (HSCT). Fibroblasts cell lines were used as a source of DNA for individuals who received HSCT. Genomic DNA from 32 subjects (5 affected and 27 unaffected) from Family A was genotyped at 909,622 single nucleotide polymorphisms (SNPs) on the Genome-Wide Human SNP 6.0 Array (Affymetrix).

2015-11-25 | E-GEOD-75314 | biostudies-arrayexpress

Affymetrix 6.0 SNP arrays interrogated to detect allele-specific DNA modification in the brain

Project description:It has long been hypothesized that knowledge of allele-specific modification (ASM; "modification" is used to denote various types of epigenetic cytosine marks, not only methylation) can supplement and inform GWAS of complex diseases and traits. To explore the relationship between GWAS subthreshold SNPs and ASM, we identified brain ASM-SNPs from Caucasian control individuals (n=76) and Caucasian patients affected by schizophrenia (n=65) or bipolar (n=67) using the Affymetrix SNP 6.0 microarray, one of the most common GWAS platforms which has also been thoroughlyt validated for ASM mapping. The brain samples (N=230, all ethnicities) were interrogated twice on Affymetrix SNP 6.0 microarrays. First, regular SNP genotyping was performed following the manufacturer's protocol. Second, we investigated allelic differences in DNA methylation by enriching the unmodified DNA fraction using DNA methylation-sensitive restriction enzymes.

2015-07-29 | E-GEOD-71443 | biostudies-arrayexpress

A missense mutation in TFRC, encoding transferrin receptor 1, causes combined immunodeficiency (Family B)

Project description:Affymetrix 6.0 SNP data for haplotype comparison of patients from two different families sharing the same homozygous mutation in TFRC, to determine if the families were related to each other Peripheral blood was used for patients who had no history of hematopoietic stem cell transplant (HSCT). Fibroblasts cell lines were used as a source of DNA for the individual who received HSCT. Genomic DNA from 3 subjects (2 from Family A, 1 from Family B in duplicate) was genotyped at 909,622 single nucleotide polymorphisms (SNPs) on the Genome-Wide Human SNP 6.0 Array (Affymetrix).

2015-11-25 | E-GEOD-75349 | biostudies-arrayexpress

Frequent and Focal FGFR1 Amplification Associates With Therapeutically Tractable FGFR1 Dependency in Squamous-cell Lung Cancer.

Project description:We analyzed 155 squamous- cell lung cancer and 77 adenocarcinoma of the lung samples using 6.0 SNP-arrays all normal tissues that were used to infer copy number are provided

2010-12-16 | GSE25016 | GEO

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