GEO DataSets

(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

(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

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) 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) 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) The Arabidopsis Pathoarray 464_001 (GPL3638) was used to compare response of wild-type, rps2-101C (Bent et al., 1994; Mindorinos et al., 1994) and ndr1-1 (Century et al., 1995) to Pseudomonas syringae strain expressing avrRpt2. The two mutants are compromised in RPS2-mediated resistance but distinct difference between them has not been described. The results suggested that ndr1-1 affects a defense signaling pathway(s) in addition to the RPS2-dependent pathway, and indicate that the microarray is a powerful tool for systems analysis of the Arabidopsis disease signaling network. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL3638

8 Samples

Download data: GPR

(Submitter supplied) To evaluate technical reproducibility of Arabidopsis Pathoarray 464_001 (GPL3638), two slides were hybridized with labeled amplified RNA prepared from identical RNA. The RNA was prepared from Pseudomonas syringae ES4326- and 5mM MgSO4- injected samples (Psm 24h set C and mock 24h set C. See also GSE4429, GSM99793 and GSM99794). Keywords: Evaluation of a custom microarray performance

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL3638

4 Samples

Download data: GPR

(Submitter supplied) In order to protect themselves from pathogens, plants activate a battery of defense pathways, many of which involve changes in gene expression. We are interested in identifying plant genes that are differentially expressed in response to pathogen exposure, with the ultimate goal of studying the roles of these genes in plant defense. Keywords: disease response

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

2 Samples

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(Submitter supplied) Oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

8 Series

30 Samples

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(Submitter supplied) Oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

2 Series

6 Samples

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(Submitter supplied) Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70/50-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

12 Series

370 Samples

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(Submitter supplied) Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

26 Series

1 Related Platform

672 Samples

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(Submitter supplied) Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

3 Series

299 Samples

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(Submitter supplied) miChip v8.0 annotation was done for human. miChip v8.0 contains capture probe matching several mouse and rat microRNAs that were not validated in human (miRbase v 8.0) miChip array are spotted on CodeLink, GE Life Science, cat. no. 30001100). Codelink glass slides are coated with N-hydroxysuccinimide Protocol: LNA-modified oligonucleotide (Exiqon) capture probes are designed to have a close to uniform Tm of 72 Celsius against their complementary targets. more...

Organism:

Homo sapiens

3 Series

50 Samples

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(Submitter supplied) Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and in house platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. more...

Organism:

Mus musculus

Type:

Expression profiling by array

9 related Platforms

91 Samples

Download data: CEL, TIFF

(Submitter supplied) Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and “in-house” platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL3734

20 Samples

Download data: TIFF

(Submitter supplied) Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and “in-house” platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL3761

5 Samples

Download data

(Submitter supplied) Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and “in-house” platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL3760

20 Samples

Download data: TIFF