Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole-genome genotyping of human islets using Illumina infinium chips

ABSTRACT: Genomic DNA was extracted from human islets using Dneasy Blood & Tissue Kit (QIAGEN) with RNase A treatment. 200-500ng DNA was genotyped using InfiniumOmni2-5-8v Genotyping BeadChips (Illumina).DNA was isolated from human islet cells from various donors. DNA was genotyped using Illumina Infinium whole-genome genotyping array. Genotypes were called with GenomeStudio (v.2.0.4) using default settings. Genotypes that passed quality filters (missing<0.05, minor allele frequency (MAF>0.01), non-ambiguous alleles defined by AT/GC variants with MAF>40%) were exported.

ORGANISM(S): Homo sapiens

PROVIDER: GSE170763 | GEO | 2023/02/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Malignant Schwann cell precursors mediate intratumoral plasticity in human neuroblastoma [Array]

Project description:we used single-cell transcriptomics and genotyping arrays to characterize 17 neuroblastoma samples across different risk groups and genetic subsets.Fresh samples, obtained from surgical resections and core biopsies, were used for genome variation profiling. DNA extraction from neuroblastoma samples was performed using the DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s protocol. DNA quality was assessed using the Tapestation platform (Agilent). SNP microarray analysis was performed using the Cytoscan HD Array (Affymetrix) and data was processed using the Chromosome Analysis Suite version 3.3.0.139.

2022-12-14 | GSE147773 | GEO

Affymetrix_SNP6_Allelotyping

Project description:Comparison of Genotyping using pooled DNA samples (Allelotyping) and Individual Genotyping using the Affymetrix Genome-Wide Human SNP Array 6.0 In this study, data from 100 DNA samples individually genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0 were used to estimate the error of the pooling approach by comparing the results with those obtained using the same array type but DNA pools each composed of 50 of the same samples. Newly developed and established methods for signal intensity correction were applied. Furthermore, the relative allele intensity signals (RAS) obtained by allelotyping were compared to the corresponding values derived from individual genotyping. Similarly, differences in RAS values between pools were determined and compared.

2013-06-22 | GSE48190 | GEO

Genotyping data of French wild boar populations using a porcine genomic beadchip array

Project description:All-genome genotyping data from French wild boar populations could be useful for diversity studies in the wild boar species as well as for phylogeny studies with domestic pig populations. The data produced in this experiment concern 362 wild boars collected between 2013 and 2019 in various French departments. The biological samples that were collected were either blood samples or ear biopsies. Genomic DNA was extracted from cells after proteinase K lysis and ethanol precipitation. DNA was hybridized on the GeneSeek Genomic Profiler porcine beadchip (GGP70K HD Porcine Illumina) using Infinium technology. Fluorescence intensity data obtained for each Single Nucleotide Polymorphism were analyzed with GenomeStudio software to infer genotypes. In addition, the raw fluorescence data could be useful for Copy Number Variation studies.

2022-01-25 | E-MTAB-10591 | biostudies-arrayexpress

Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays [Omni1-Quad]

Project description:To better understand the natural history of bone marrow failure syndromes, we analyzed 124 single nucleotide polymorphism arrays (SNP-A) from a comprehensively characterized cohort of 91 patients who had SNP-A for clinical evaluation of BMFS. 67 samples from 51 patients were genotyped with the Quad610, and 57 samples from 54 patients were genotyped with the Omni1-Quad. This submission includes 55 samples from 54 patients that were genotyped with Omni1-Quad. Illumina Infinium SNP-A genotyping was performed on DNA extracted from bone marrow aspirates using standard manufacturer's protocol

2014-01-01 | E-GEOD-48482 | biostudies-arrayexpress

Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays [Illumina Quad610 Beadchip]

Project description:To better understand the natural history of bone marrow failure syndromes, we analyzed 124 single nucleotide polymorphism arrays (SNP-A) from a comprehensively characterized cohort of 91 patients who had SNP-A for clinical evaluation of BMFS. 67 samples from 51 patients were genotyped with the Quad610, and 57 samples from 54 patients were genotyped with the Omni1-Quad. This submission includes 67 samples from 51 patients that were genotyped with Illumina Quad610 Beadchip. Illumina Infinium SNP-A genotyping was performed on DNA extracted from bone marrow aspirates using standard manufacturer's protocol

2014-01-01 | E-GEOD-48483 | biostudies-arrayexpress

Plasmodium falciparum assocation study of artemisinin resistance

Project description:A testing association of parasite genotypes with clinical resistance phenotype. Submission of genotypes from all microarray genotyped samples

2014-05-28 | GSE56390 | GEO

Plasmodium falciparum custom resequencing array testing and validation

Project description:A custom resequencing array for analysis of field isolates of plasmdium falciparum was created. Test of DNA with genotypes known at all loci genotyped by the microarray as well as test of accuracy correlation with amounts of DNA added to each array

2014-03-28 | GSE56305 | GEO

SNP_array

Project description:33 ETMR samples were genotyped using Illumina HumanOmni2.5M array. Hybridization and scanning was done according to the manufacturer's instructions (Illumina). Copy number (Log R) and B allele frequency estimates were obtained sing the Genotyping module (v1.9.4) in GenomeStudio v2011.1 (Illumina). Normalized and log2-transformed copy number measurements were imported from genomestudio and analysed using R package CopyNumber to identify segments with similar copy number.

| EGAD00010001667 | EGA

Affymetrix_SNP6_Allelotyping

2013-06-22 | E-GEOD-48190 | biostudies-arrayexpress

Genome wide analysis of acral melanoma (Affymetrix)

Project description:Genotyping of a matched normal, primary and metastatic acral melanoma DNA from blood and one matched Primary and one metastatic acral melanoma was genotyped on Affmetrix SNP6

2011-12-13 | E-GEOD-28910 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data