Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 786
Release date: Jul 1 2016
Last update date: Aug 13 2018
Access: Public
Dataset link Characterization of expression quantitative trait loci in extensively phenotyped pedigrees from Colombia and Costa Rica

Experimental Protocol


Lymphoblastoid cell lines (LCLs) were established by in vitro infection of peripheral blood mononuclear cells with Epstein Barr virus, and RNA was extracted from these cell lines and its expression quantified using Illumina Human HT-12 v4.0 Expression BeadChips. Expression values were background corrected, quantile normalized, log2 transformed, and corrected for major known batch effects. The outcome of these procedures is what we refer to as ‘probe expression’ for all subsequent analyses. After quality control filters, the 34,030 probes included in the final set were uniquely aligned to hg19, contained no common SNPs (as defined in dbSNP 137 or 138), queried 24,385 unique genes, and their expression was detected in at least one individual. For a detailed description of the processing steps used at each site and the RNA quantification, normalization, and quality control procedures, see the supplementary note. Please note that charateristics FID, IID and DiagnosisBP1 represents family ID, individual ID and BP1 diagnosis (0= no BP1, 2= BP1), respectively.

Repositories


GEO

GSE82042

ArrayExpress

E-GEOD-82042

BioProject

PRJNA323740

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Contact


Giovanni Coppola