Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

Abstract

The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

Human CD8+EMRA T cells display a senescence‐associated secretory phenotype regulated by p38 MAPK

“…Principal component analysis was generated using the Partek software package. The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (Edgar et al ., 2002) and are accessible through GEO Series accession number GSE98640 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98640). …”

Suppression of proinvasive RGS4 by mTOR inhibition optimizes glioma treatment

“…Differentially expressed genes were identified using the implemented empirical Bayes method (Smyth, 2004) with adjustment for multiple testing according to Benjamini-Hochberg and a significance threshold of p < 0.05. Array data have been deposited in NCBI's Gene Expression Omnibus (GEO) (Edgar et al, 2002) and are accessible through GEO Series accession number GSE24232 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=G…”

Differentially expressed genes during malting and correlation with malting quality phenotypes in barley (Hordeum vulgare L.)

“…Twenty-two arrays were analyzed with two biological replications per cultivar per time point, with the exception of Merit day 4 with three replications and Harrington day 1, where one of the replicates was discarded (Table 1). All microarray data have been deposited in NCBI's Gene Expression Omnibus (Edgar et al 2002) and are accessible through GEO Series accession number GSE11200 (http://www.ncbi.nlm.nih.gov/geo/query/acc. cgi?acc=GSE11200) ( Table 1).…”