GEO DataSets

(Submitter supplied) To define the parameters necessary to design short oligo arrays for maize (Zea mays L.), a species with particularly high nucleotide (SNP) and insertion-deletion (indel) polymorphism frequencies, gene expression was analyzed in for four maize inbred lines using a custom Affymetrix DNA array. Statistically significant interactions between probes and maize inbreds were detected, affecting five or more probes (out of 30 probes per transcript) in the majority of cases, indicating the effect of polymorphisms on gene expresison estimates using this platform. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL3618

24 Samples

Download data: CEL

(Submitter supplied) Affymetrix U133 Plus 2.0 arrays were hybridized with varying amounts of starting material to determine whether different measurements of gene expression were observed. Keywords: Affymetrix starting material study

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2204

Platform:

GPL570

12 Samples

Download data: CEL

(Submitter supplied) Stratagene universal human RNA hybridized to both U133 Plus 2.0 and U133 A arrays. Keywords: Affymetrix platform comparison

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL570

10 Samples

Download data: CEL

Analysis of 1, 2, 5 or 10 ug of Stratagene universal human reference RNA as starting material. Results provide insight into the influence of starting RNA quantity on the subsequent gene expression signal measured from a microarray.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 protocol sets

Platform:

GPL570

Series:

GSE3062

12 Samples

Download data: CEL

(Submitter supplied) Heterosis (hybrid vigor) refers to the superior performance of hybrid progeny relative to their parents. Although widely exploited in agriculture, the mechanisms responsible for heterosis are not well understood. As a monoecious organism, a given maize plant can be used as both male and female parents of crosses. Regardless of the cross direction, the maize inbred lines B73 and Mo17 produce hybrids that substantially out-perform their parents. more...

Organism:

Zea mays

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

4 related Platforms

533 Samples

Download data: TXT

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL5175 GPL5188

40 Samples

Download data: CEL

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

20 Samples

Download data: CEL

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

20 Samples

Download data: CEL

(Submitter supplied) BACKGROUND: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by genome tiling array; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL4012 GPL201 GPL2641

40 Samples

Download data: CEL, GPR

(Submitter supplied) Background: Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed with Affymetrix porcine microarrays is presented. A linear mixed model analysis was used to identify significant breed-by-probe interactions. Results: Gene specific linear mixed models were fit to each of the log2 transformed probe intensities on these arrays, using fixed effects for breed, probe, breed-by-probe interaction, and a random effect for array. more...

Organism:

Sus scrofa

Type:

Expression profiling by genome tiling array

Platform:

GPL6472

6 Samples

Download data: CEL

(Submitter supplied) Background: Genome-wide detection of single feature polymorphisms (SFP) in swine using transcriptome profiling of day 25 placental RNA by contrasting probe intensities from either Meishan or an occidental composite breed with Affymetrix porcine microarrays is presented. A linear mixed model analysis was used to identify significant breed-by-probe interactions. This dataset uses different tissue types to explore the consequences of additional sample variance. more...

Organism:

Sus scrofa

Type:

Expression profiling by genome tiling array

Platform:

GPL6472

6 Samples

Download data: CEL

(Submitter supplied) Comparison of mRNA accumulation in segregating doubled haploid barley lines ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, . The equivalent experiment is BB21 at PLEXdb.]

Organism:

Hordeum vulgare

Type:

Expression profiling by array

Platform:

GPL1340

41 Samples

Download data: CEL

(Submitter supplied) Both spotted long oligonucleotide arrays (GPL1384) and Affymetrix GeneChip arrays (GPL96) were used to analyze gene expression in six human head and neck squamous cell carinoma samples versus control samples or lymph node metastases of the same patients. Hybridizations of HG-U133A GeneChip arrays were performed using standard Affymetrix protocols and equipment. Before hybridization on DKFZ Operon 27k long oligonucleotide arrays, 2 µg RNA were amplified by one round of linear isothermal RNA amplification, followed by Cy-dUTP incorporation using Klenow fragment. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL1384 GPL96

24 Samples

Download data: CEL, TIFF

(Submitter supplied) Studying the causes and correlates of natural variation in gene expression in healthy populations assumes that individual differences in gene expression can be reliably and stably assessed across time. However, this is yet to be established. We examined 4-hour test-retest reliability and 10 month test-retest stability of individual differences in gene expression in 10 12-year-old children.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

36 Samples

Download data: CEL