GEO DataSets

(Submitter supplied) see Methods section of related Citation (PMID: 16164747).

Organism:

Salmo salar

5 Series

240 Samples

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(Submitter supplied) Gene selection Microarray fabrication is described in detail in von Schalburg et al. 2005 (BMC Genomics 6:126). Selection criteria for unique Atlantic salmon (AS) and rainbow trout (RT) cDNAs for inclusion on the 16K microarray were as follows: ESTs (cDNA fragments) were assembled into contiguous sequences (contigs) by PHRAP under stringent clustering parameters (minimum score: 100; repeat stringency: 0.99). more...

Organism:

Salmo salar

1 Series

6 Samples

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(Submitter supplied) Comparison of gene expression of infected versus non infected Salmo salar gill tissue over time. The time course includes 0 hr, 44 hr, 114 hr and 189 hr post infection Keywords: Infected vs control

Organism:

Osmerus mordax; Oncorhynchus mykiss; Coregonus clupeaformis; Oncorhynchus tshawytscha; Salmo salar

Type:

Expression profiling by array

Platform:

GPL2716

12 Samples

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(Submitter supplied) From a set of 15 standard, normalized or full-length cDNA libraries, we generated 139 007 3'- or 5'-end sequenced ESTs, representing more than one-third of the c. 385 000 publicly available Populus ESTs. Clustering and assembly of 107 519 3'-end ESTs resulted in 14 451 contigs and 20 560 singletons, altogether representing 35 011 putative unique transcripts, or potentially more than three-quarters of the predicted c. more...

Organism:

Populus trichocarpa x Populus deltoides; Populus

Type:

Expression profiling by array

Platform:

GPL5921

10 Samples

Download data: TIFF

(Submitter supplied) Corning UltraGaps Protocol: The 15,496 clones from 14 poplar cDNA libraries (Ralph et al., 2006) were selected based on a CAP3 assembly (Huang and Madan, 1999; 95% identity and 40 bp overlap) of ca. 37,000 high-quality 3’ ESTs (i.e. longest available EST sequence from each putative unique transcript). Following in silico selection of candidates, clones were robotically rearrayed from daughter glycerol stock 384-well plates into 96-well plates prefilled with 7% glycerol in LB + ampicillin, incubated overnight at 37°C, and checked for uniform optical density. more...

Organism:

Populus

8 Series

158 Samples

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(Submitter supplied) Initial test of the NBFGC cDNA microarray. Keywords = bovine, cDNA, microarray, false positive Keywords: repeat sample

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL325

6 Samples

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(Submitter supplied) Lung, liver, muscle (Semitendinosus), small intestine (duodenum; approximately 5 cm from stomach) were collected from six cross-bred white pigs (three 15 week old and three 17 week old). Total RNAs were isolated from these tissues to study gene expression by using the first generation of porcine long oligonucleotide microarray. In the experimental design, tissue samples from the six animals were assigned to six loops (three for younger animals and three for older animals). more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL1881

24 Samples

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(Submitter supplied) Zhao SH, Recknor J, Lunney JK, Nettleton D, Kuhar D, Orley S, Tuggle CK: Validation of a first-generation long-oligonucleotide microarray for transcriptional profiling in the pig.Zhao SH, Recknor J, Lunney JK, Nettleton D, Kuhar D, Orley S, Tuggle CK., Genomics. 2005 Nov;86(5):618-25. Protocol: Oligonucleotides were printed in duplicate on epoxide slides by operon. Operon probes are designed from The TIGR Gene Index Database SsGI Release 5.0 released 10/1/02. more...

Organism:

Sus scrofa

1 Series

18 Samples

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(Submitter supplied) This is a chicken multi-tissue cDNA microarray with 12752 elements. It comprises clones from chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. Sequence information is available from GenBank for all features on the array. Protocol: The clone-set was amplified in 96 well plates and re-arrayed into a 384-well Montage (Millipore) filtration plate to isolate the amplified DNA products. more...

Organism:

Gallus gallus

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(Submitter supplied) Background The application of microarray technology to functional genomic analysis in the chicken has been limited by the lack of arrays containing large numbers of genes. Results We have produced cDNA arrays using chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. From a total of 363,838 chicken ESTs representing 24 different adult or embryonic tissues, a set of 11,447 non-redundant ESTs were selected and added to an existing collection of clones (4,162) from immune tissues and a chicken bursal cell line (DT40). more...

Organism:

Gallus gallus

5 Series

60 Samples

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(Submitter supplied) Development of a Large-Scale Chemogenomics Database to Improve Drug Candidate Selection and to Understand Mechanisms of Chemical Toxicity and Action These data support the publication titled "Development of a Large-Scale Chemogenomics Database to Improve Drug Candidate Selection and to Understand Mechanisms of Chemical Toxicity and Action" Copyright (c) 2005 by Iconix Pharmaceuticals, Inc. Guidelines for commercial use: http://www.iconixbiosciences.com/guidelineCommUse.pdf Keywords: other

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS1429

Platform:

GPL1820

69 Samples

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Analysis of livers of Sprague-Dawley males treated with the anticancer drug carmustine, methotrexate, or thioguanine. Animals treated daily with various doses and livers examined at various time points up to 5 days. Results combined with clinical pathology assessments in a chemogenomics database.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, transformed count, 3 agent, 6 dose, 4 time sets

Platform:

GPL1820

Series:

GSE2409

69 Samples

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(Submitter supplied) series of experiments assesing false positive and background of pig brain library (PBL) microarray Keywords = porcine brain, pig brain Keywords: repeat sample

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL336

2 Samples

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(Submitter supplied) Fish and Chips: Expression Profiling in Non-traditional Model Systems Using a Cichlid Fish cDNA Microarray This series represents the 26 arrays that went into Renn et al 2004 (submitted January 16th), and one additional hybridization (GSM15240) that was not included in the publication analysis for statistical reasons. Keywords: other

Organism:

Salmo salar; Danio rerio; Xiphophorus; Haplochromis burtoni; Neolamprologus brichardi; Xenotilapia melanogenys; Poecilia reticulata; Oreochromis niloticus

Type:

Expression profiling by array

Platform:

GPL928

27 Samples

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(Submitter supplied) The copepod, Calanus finmarchicus is a keystone species for the North Atlantic. Because of recent changes in the geographic distribution of this species, there are questions as to how this organism responds physiologically to environmental cues. Molecular techniques allow for examination and new understanding of these physiological changes. Here, we describe the development of a microarray for high-throughput studies of the physiological ecology of C. more...

Organism:

Calanus finmarchicus

Type:

Expression profiling by array

Platform:

GPL14742

11 Samples

Download data: GPR

(Submitter supplied) We designed a custom expression 8x15 k microarray for Cottus fishes based on transcriptome sequencing. It is a known fact, that oligonucleotide probes differ in the binding behavior towards their target sequences. Therefore, we performed a calibration of our microarray where we assessed the binding behavior of the individual probes empirically. This information was used to normalize gene expression data measurements with the same microarray in another experiment. more...

Organism:

Cottus

Type:

Expression profiling by array

Platform:

GPL15378

7 Samples

Download data: TXT

(Submitter supplied) European sculpins (Cottus) harbor an example of a recent hybrid speciation event, which entails the invasion of a new habitat by the hybrid species. We compare the transcriptomes of both parental species and the hybrid species to understand how they differ. F2 crosses between the parent species are compared to the hybrid species and its parent species to identify unique patterns of the hybrid species due to the initial hybridization process or respectively to other processes. more...

Organism:

Cottus; Cottus perifretum; Cottus rhenanus

Type:

Expression profiling by array

Platform:

GPL15375

56 Samples

Download data: TXT