GEO DataSets

(Submitter supplied) Yeast knockout collection TAG microarrays are an emergent platform for rapid, genome-wide functional characterization of yeast genes. We describe a method for analyzing two-color array data to efficiently represent differential knockout strain representation across two experimental conditions. Using a fully defined spike-in pool, we show that the sensitivity and specificity of this method exceed typical current approaches. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platform:

GPL1444

5 Samples

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(Submitter supplied) Comprehensive array (June 2002) of all 6018 UpTag/DnTag pairs incorporated into deletion constructs in the Yeast Knockout strain collection Same as GPL1444, but with one gene per table row Protocol: In-situ synthesis using inkjet printing technology

Organism:

Saccharomyces cerevisiae

1 Series

981 Samples

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(Submitter supplied) Comprehensive array of all 6018 UpTag/DnTag pairs designed for incorporation into yeast deletion strains by the Yeast Deletion Project (June 2002). Custom-designed negative and positive controls comprise almost half of the 215x105 array. Keywords = yeast, deletion, knockout, tag, barcode, synthetic, control, oligonucleotide

Organism:

Saccharomyces cerevisiae

16 Series

218 Samples

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(Submitter supplied) See Talla et al. 2003 (PMID : 14499002)

Organism:

Saccharomyces cerevisiae

1 Series

22 Samples

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(Submitter supplied) See Talla et al. 2003 (PMID : 14499002)

Organism:

Saccharomyces cerevisiae

1 Series

18 Samples

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(Submitter supplied) The yeast 5803 ORFs MicroArray is composed of 32 subgrids, which follow a pattern of 8 metarows and 4 metacolumns. Each subgrid contains 20 columns and 20 rows with a dot spacing of 200 µm. Probes are spotted as closed duplicates. In order to provide a friendly environment, the first subgrid row on each array metarow contains all the normalization controls, which include the controls with serial dilution of the Renilla LuxA cDNA PCR product. more...

Organism:

Saccharomyces cerevisiae

3 Series

16 Samples

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(Submitter supplied) The yeast 5803 ORFs MicroArray is composed of 32 subgrids, which follow a pattern of 8 metarows and 4 metacolumns. Each subgrid contains 20 columns and 20 rows with a dot spacing of 200 µm. Probes are spotted as closed duplicates. In order to provide a friendly environment, the first subgrid row on each array metarow contains all the normalization controls, which include the controls with serial dilution of the Renilla LuxA cDNA PCR product. more...

Organism:

Saccharomyces cerevisiae

1 Series

6 Samples

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(Submitter supplied) Microarray karyotyping (aCGH) of three independent isolates each of four different commerical wine yeast strains was performed. Duplicate arrays (labeled "A" and "B") were performed for each isolate. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platforms:

GPL2634 GPL2633

24 Samples

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(Submitter supplied) These datasets use diploid-based synthetic lethality analysis on microarrays (dSLAM) as a new technology for identifying genetic interactions of various types. These interactions include synthetic lethality (CIN8, BIM1, SGS1), synthetic haploinsufficiency (TUB1), dosage suppression (LCD1), suppression of a lethal mutation (SML1), suppression of an overexpressed conditionally lethal allele (CDC102), and gene-chemical interactions (Benomyl). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL1446 GPL1444 GPL1445

33 Samples

Download data: TIFF

(Submitter supplied) Comparison of the transcriptomes of Saccharomyces cerevisiae wild type FY23 and a PDE2 deletion mutant DJ28. Keywords = PDE2 Keywords = Ras/cAMP pathway Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL422

10 Samples

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(Submitter supplied) GMAP-UTS520601 array

Organism:

Homo sapiens

1 Series

621 Samples

Download data: CDF, TXT

(Submitter supplied) Purified DNA of some 4600 overlapping shotgun clones in vector pCR-BluntII-TOPO (Invitrogen, Groningen, The Netherlands) was used as template in standard PCR amplification with the vector-specific primer pair d(TCGGATC CACTAGTAACG) and d(GGCCGCCAGTGTGATG). Shotgun cloning had been performed according to the procedures described by the vector's manufacturer. Each PCR reaction was individually checked by agarose gel electrophoresis. more...

Organism:

Pseudomonas putida

1 Series

6 Samples

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(Submitter supplied) Schizosaccharomyces pombe 4976 ORFs spotted in duplicate on glass slide Keywords = yeast ORF DNA microarray Reference: Xue Y, Haas SA, Brino L, Gusnanto A et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 2004 Jan 15;21(1):25-39. PMID: 14745780 Protocol: Primary PCR: The PCR reactions are performed using tagged genome specific primers in the presence of genomic DNA (provided by your laboratory). more...

Organism:

Schizosaccharomyces pombe

3 Series

3 Samples

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(Submitter supplied) Schizosaccharomyces pombe 4976 ORFs spotted in duplicate on glass slide Keywords = yeast ORF DNA microarray Protocol: Primary PCR: The PCR reactions are performed using tagged genome specific primers in the presence of genomic DNA (provided by your laboratory). We normally achieve a success rate of 93 % of PCR reactions. For the failed PCR reactions we perform three different protocols of PCR conditions, which include different MgCl2 concentrations and different Taq polymerase. more...

Organism:

Schizosaccharomyces pombe

4 Series

14 Samples

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(Submitter supplied) Schizosaccharomyces pombe 4976 ORFs spotted in duplicate on glass slide Keywords = yeast ORF DNA microarray

Organism:

Schizosaccharomyces pombe

1 Series

2 Samples

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(Submitter supplied) DNA microarray technology allows the analysis of genome structure and dynamics at genome-wide scale. Expression microarrays (EMA) contain probes for annotated open reading frames (ORF) and are widely used for the analysis of differential gene expression. By contrast, tiling microarrays (TMA) have a much higher probe density and provide unbiased genome-wide coverage. The purpose of this study was to develop a protocol that would take advantage of the high resolution of TMAs for quantitative measurement of DNA strand-specific differential expression of annotated and non-annotated transcripts. more...

Organism:

Schizosaccharomyces pombe; Schizosaccharomyces pombe 972h-

Type:

Expression profiling by array; Expression profiling by genome tiling array

Platforms:

GPL9672 GPL9671

8 Samples

Download data: CEL

(Submitter supplied) A ruler array combines novel sample preparation protocols, tiling genomic microarrays, and a new computational method to turn each probe on a microarray into a ruler that measures the physical distance between defined genomic sequences regardless of the intervening sequence. The ruler array protocol involves (1) genomic DNA purification (2) digestion with a restriction enzyme (3) ligation of a biotinylated adapter molecule to the cut sites (4) purification on streptavidin beads (5) polymerase extensions from a primer complementary to the adapter using labeled dNTPs and (6) hybridization to a tiling microarray

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4130

2 Samples

Download data: TXT

(Submitter supplied) To systematically characterize the phenotypic behavior of two 'prototrophic' version of the Yeast Knockout (YKO) gene deletion collection, we compared genome-wide finess assays across a diverse set of drug and environmental conditions. This analysis uncovered experimental liabilities in the the prototrophic collections distinct from the YKO auxotrophies that shows that auxotrophic repair (regardless of methodology) does not restore wildtype behaviour.

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platform:

GPL17030

236 Samples

Download data: CEL

(Submitter supplied) Small G1 daughter yeast cells were isolated by centrifugal elutriation. They were then released into YEP ethanol, and followed through one cell cycle, with samples being taken every 30 minutes. This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97 Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS39

Platform:

GPL59

14 Samples

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(Submitter supplied) Yeast cells were blocked in telophase using a cdc15-2 temperature senstive mutant at restrictive temperature. The culture was then shifted to permissive temperature (25oC), and released into the cell cycle. Samples were then taken during the course of almost three full cell cycles. This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97 Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL62

25 Samples

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