GEO DataSets

(Submitter supplied) Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL5

8 Samples

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(Submitter supplied) The array was assembled using 1,681 testes ESTs, representing 1,527 Drosophila melanogaster EST sequences and 144 anonymous clones from the bs collection (CLONE_ID). An aliquot of the same DNA preparation used in the sequencing reactions (GB_ACC), diluted 2/50 in TE, provided material for the PCRs. Inserts were PCR amplified (1X PCR buffer [Life Technologies], 1.5 mM MgCl2, 0.2 mM dNTPs, 1 µM T7 22-mer primer, 1 µM T3 20-mer primer, 2 µl of plasmid DNA dilution [approximately 10 ng], 0.035 U/µl recombinant Taq DNA polymerase [Life Technologies], in a volume of 100 µl, cycled 94C 2 min, 30X[94 C 0.5 min, 55 C 0.5 min, 2.5 min 72 C], 10 min 72 C in a PTC-225 DNA Engine Tetrad [MJ Research]), and successful amplification was confirmed by agarose gel electrophoresis (PCR-QC: passed = product present, failed = no product). more...

Organism:

Drosophila melanogaster

1 Series

8 Samples

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(Submitter supplied) Time course analysis series in Development of the transcriptome from Drosophila melanogaster using the Heidelberg FlyArray. All stages were hybridized against embryonic stage 0-4 h as reference control. Keywords: time-course

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL517

24 Samples

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(Submitter supplied) Comparisons of gene expression profiles between testis and ovary of juvenile and wild brooders were made through a cDNA microarray in the black tiger shrimp (Penaeus monodon). Differentially expressed genes were identified through the microarray analysis, and the microarray results were confirmed by real-time PCR. Selected genes were further characterized.

Organism:

Penaeus monodon

Type:

Expression profiling by array

Platform:

GPL10413

9 Samples

Download data: GPR

(Submitter supplied) Identification of testis-relevant genes using in silico analysis from testes ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon) A total of 4,803 ESTs from the testis library were unidirectionally sequenced and analyzed in silico using a customizable data analysis package, ESTplus. A total of 2,702 unique sequences from 424 contigs and 2,278 singletons were identified. Approximately, 1,134 sequences from the total of 2,702 unique sequences (contigs and singletons) are homologous to genes with known functions. more...

Organism:

Penaeus monodon

Type:

Expression profiling by array

Platform:

GPL9679

3 Samples

Download data: GPR

(Submitter supplied) Eye-stalks of some flies exhibit extreme sexual dimorphism, but little is known about the genetic mechanisms producing variation in these ornamental traits. Therefore, we constructed an EST database of genes expressed in the developing eye-antennal imaginal disc of the highly dimorphic species, Teleopsis dalmanni, and used this set of genes to construct high density oligoarrays and compare patterns of gene expression between lines of flies selected for divergent eyespan. more...

Organism:

Teleopsis dalmanni

Type:

Expression profiling by array

Platform:

GPL8358

8 Samples

Download data: GPR

(Submitter supplied) Each 44K array contains 9 features for each of ~3600 genes that have been identified in an EST study of eye-antennal discs from late instar larvae or pupae of a diopsid stalk-eyed fly. cDNA clusters were included that had 1) significant homology to known genes in Drosophila or Anopheles, 2) an ORF larger than 300 bp (labeled ORF-) or 3) more than four associated cDNA clones (labeled X-). Three 60 bp oligonucleotide probes were designed for each gene based on the consensus sequence with the highest Blast hit or largest ORF within each cluster. more...

Organism:

Teleopsis dalmanni

1 Series

8 Samples

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(Submitter supplied) The expression profiles of Drosophila Kc167 and SL2 cells were compared on the CDMC_Drosophila_7k2 array platform. Three independent RNA samples from each cell line were isolated and compared in a pairwise fashion. Dye-flip experiments were also performed. See Neal et al. 2003 for results and discussion. Keywords = Kc167 Keywords = SL2 Keywords = Drosophila Keywords: other

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL311

6 Samples

Download data: TIFF

(Submitter supplied) A large batch of Drosophila Kc167 total RNA was prepared and was used for 3 homotypic hybridizations in order to evaluate the inter-slide variability using the CDMC_Drosophila_7k2 platform. See Neal et al. 2003 for results and discussion. Keywords = Kc167 Keywords = Drosophila Keywords = Platform Variability Keywords: other

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL311

3 Samples

Download data: TIFF

(Submitter supplied) Three different amounts, 20 ug (GSM6155), 40 ug (GSM6157) and 80ug (GSM6158), of total Kc167 RNA were used in homotypic labelings to determine the optimal amount of RNA necesary to produce the most useable data using the CDMC_Drosophila_7k2 array. See Neal et al. 2003 for results and discussion. Keywords = Kc167 Keywords = Drosophila Keywords = RNA amount Keywords: other

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Dataset:

GDS374

Platform:

GPL311

3 Samples

Download data: TIFF

(Submitter supplied) The CDMC_Drosophila_7K2 array is a primarily cDNA-based Drosophila melanogaster glass microarray. The array features 5,756 Berkeley Drosophila Genome Project cDNAs, 1,078 NIH Testis cDNAs (Andrews et al. 2000) and 546 gene fragments that were amplified from genomic DNA, together representing approximately 50% of the predicted genes in D. melanogaster. The array is produced by the Canadian Drosophila Microarray Centre at the University of Toronto and is available for distribution to academic labs. more...

Organism:

Drosophila melanogaster

1 DataSet

5 Series

19 Samples

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Analysis of the effect of varying starting quantity of RNA. Three different amounts, 20 ug, 40 ug and 80 ug total Kc167 RNA used in homotypic labelings to determine optimal quantity of RNA.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array, log ratio, 3 protocol sets

Platform:

GPL311

Series:

GSE417

3 Samples

Download data: TIFF

(Submitter supplied) Investigatation into how genes with sex-differential expression profiles are distributed among the chromosomes in Drosophila. Assayed the expression of 14,142 predicted transcripts in competitive hybridizations and found a dramatic underrepresentation of X-chromosome genes showing high relative expression in male. This is the first report of sex-biased expression of the full (predicted) genome. Findings indicate that there is significant sex-biased expression, especially in gonads. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL20

46 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) 10,185 high-quality sequences were obtained from 10 tissue(or stage of development)-specific libraries and were submitted to GenBank (accession numbers: FF281814-FF291996) The final array design contained 5,087 gene specific Solea senegalensis probes, as well as positive and negative control probes (maize expansin, ZmMYB42, and xyloglucan endo-transglycosylase), a total of 700 per array. These were used to assess detection limits and range, to verify spatial homogeneity, and to determine experimental within-array variation. more...

Organism:

Solea senegalensis

10 Series

21 Samples

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(Submitter supplied) SAGE libraries generated from total testes of adult mouse males. Keywords = testis Keywords: other

Organism:

Mus musculus

Type:

Expression profiling by SAGE

Platform:

GPL11

2 Samples

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(Submitter supplied) 60-mer oligonucleotide probes were designed from EST contigs derived from Karenia brevis cDNA libraries using Array Designer v 4.0 following Agilent's recommendations for Tm, GC content, and position. Probes were submitted to Agilent's eArray website for randomization and addition of control probes. For details on printing see Agilent's website www.agilent.com. 60-mer oligonucleotide probes were designed from EST contigs derived from Karenia brevis cDNA libraries using Array Designer v 4.0 following Agilent's recommendations for Tm, GC content, and position. more...

Organism:

Karenia brevis

5 Series

78 Samples

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(Submitter supplied) Comparison of gene expression in wild type, Oregon[R], Antennapedia[73b], Apterous[56f] Drosophila melanogaster strains. Keywords: other

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL20

36 Samples

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(Submitter supplied) Drosophila melanogaster adult flies fed on food containing 16 mg/ml of pentylenetetrazole (PTZ) in the food show a hyperkinetic behavior within 24 hours. Half of that concentration, i.e., 8 mg/ml, of PTZ, if fed for seven days, though doesn’t cause seizure-like behavior, results in a decreased climbing speed in flies. This change in locomotor behavior is progressive and becomes significant only on seventh day of the treatment. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL3603

28 Samples

Download data: GPR