Screening for candidate clock-controlled genes
Ontology highlight
ABSTRACT:
ORGANISM(S): Thermosynechococcus vestitus BP-1
PROVIDER: GSE2114 | GEO | 2004/12/29
SECONDARY ACCESSION(S): PRJNA91773
REPOSITORIES: GEO
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Project description:Microarrays were hybridized with a mixture of solutions containing LL2 cDNA labeled with Cy3 or Cy5 (dye-swap) and LL14 cDNA labeled with Cy5 or Cy3 (dye-swap).
2010-05-27 | E-GEOD-2114 | biostudies-arrayexpress
Project description:Liver from five Holstein cows fed to current National Research Council (2001) recommendations during the dry period and early lactation was biopsied at -65, -30, -14, 1, 14, 28, and 49 days relative to parturition. cDNA from liver and a reference standard (made from cattle tissues not including liver or mammary) were labeled with Cy3 or Cy5 fluorescent dye and co-hybridized to our 7,872 bovine cDNA microarray using a dye-swap design. More than 5,000 sequences present on the array were expressed in liver. Normalized log-transformed ratios (liver/reference) were analyzed using a MIXED model in SAS. Keywords: cow, liver, lactation, microarray, periparturient period Keywords: time-course
2005-08-10 | GSE2692 | GEO
Project description:Chaperones have essential role in assist nascent peptides folding, prevent proteins aggregation and maintain cellular protein homeostasis. Considering spatial and temporal features of chaperones regulating in vivo, changes in single or combined chaperone-depleted E.coli strain is needed to be put into understand at transcriptional level. Here, we utilized expression microarrays to investigate global transcriptional response upon deletion of single or multiple chaperones in E. coli for understanding the transcriptional network affected by chaperones. To identify prokaryotic expression profiles in deletion of chaperones, several E.coli mutants were constructed in the following: Z116 (△tig 37℃), Z125(△dnaK37℃), Z625(△tig△dnaK 37℃ or 30℃), Z629(△tig△dnaK 30℃), NM (C-domain of tig was deleted 37℃), MC (N-domain of tig was deleted 37℃), NC (M-domain of tig was deleted 37℃). Two types of cDNA mixtures containing Cy3-labeled (or Cy5-labeled) control DNA (from BW25113) and Cy5-labeled (or Cy3-labeled) DNA targets (from mutant strain) were hybridized with E.coli microarrays in a dye-swap strategy.
2015-06-18 | GSE69912 | GEO
Project description:The purpose of the McrBC methylation microarray assay is to determine which regions of a genome are methylated versus those that are unmethylated in a single Arabidopsis thanliana genotype. McrBC is a methylation-sensitive enzyme that restricts DNA only at purine-Cmethyl half sites when separated between 50bp and 3kb. A designated amount of DNA from a particular genotype is sheared to a size range of 1kb-10kb using nebulization. We restrict half of the nebulized DNA with McrBC, and the methylated fraction is then removed from the unmethylated fraction through gel purification of DNA fragments greater than 1kb.* The remaining nebulized DNA is subjected to the same gel purification scheme, but with no McrBC treatment. In a single hybridization, the untreated sample is labeled with Cy5 and the McrBC-treated sample with Cy3. Thus, after labeling and microarray hybridization, the ratio of normalized Cy5 to normalized Cy3 represents the relative methylation at the sequence represented by the spot on the microarray. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively. The two samples in this series are complementary hybridizations in a dye-swap analysis. This is the normalized result of the paired dye swap samples VC121 and VC127. The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. These samples were not subjected to hypothesis testing. Therefore, P-values are reported as -1 and no features are flagged as significantly methylated. Keywords: other
2004-06-12 | GSE1329 | GEO
Project description:The keratinocyte cell line HaCaT was cultured for three days (proliferation) or for ten days (differentiation). RNA from cells at day3 was compared to RNA from cells at day10. The microarray hybridizations were performed in dye-swap procedure : RNA from cells at day3 was labeled with Cy3 (GSM4674, GSM4675, GSM4682, GSM4683) and then with cy5 (GSM4680, GSM4681). Keywords = cell density differentiation program in human keratinocytes Keywords: repeat sample
2003-03-11 | GSE336 | GEO
Project description:Binding of in vitro synthesized HAC1 mRNA was studied using protein microarray. 3 replicates, plus 3 reverse dye replicates An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. is_reverse: no: HAC1 mRNA Cy5 labeled; yes: HAC1 mRNA Cy3 labeled
2012-11-15 | GSE33750 | GEO
Project description:The purpose of the McrBC methylation microarray* assay is to determine which regions of a genome are methylated versus those that are unmethylated in a single Arabidopsis thanliana genotype. McrBC is a methylation-sensitive enzyme that restricts DNA only at purine-Cmethyl half sites when separated between* 50bp and 3kb. A designated amount of DNA from a particular genotype is sheared to a size range of 1kb-10kb using nebulization. We restrict half of the nebulized DNA with McrBC, and the methylated fraction is then removed from the unmethylated fraction through gel purification of DNA fragments greater than 1kb.* The remaining nebulized DNA is subjected to the same gel purification scheme, but with no McrBC treatment. In a single hybridization, the untreated sample is labeled with Cy5 and the McrBC-treated sample with Cy3.* Thus, after labeling and microarray hybridization, the ratio of normalized Cy5 to normalized Cy3 represents the relative methylation at the sequence represented by the spot on the microarray.* Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively. The two samples in this series are complementary hybridizations in a dye-swap analysis. wild-type seedlings, 9 days old. Below is the normalized result of the paired dye swap samples VC134 and VC136. The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity. To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using both family-wise error rate (FWER) and false discovery rate (FDR) controlling methods. The step-down multiple comparisons procedure of Holm (1979) was used to control the FWER below alpha = 0.01, while the step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent. Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the last two columns. Keywords: other
2004-06-12 | GSE1332 | GEO
Project description:The purpose of the McrBC methylation microarray assay is to determine which regions of a genome are methylated versus those that are unmethylated in a single Arabidopsis thaliana genotype. McrBC is a methylation-sensitive enzyme that restricts DNA only at purine-Cmethyl half sites when separated between 50bp and 3kb. A designated amount of DNA from a particular genotype is sheared to a size range of 1kb-10kb using nebulization. We restrict half of the nebulized DNA with McrBC, and the methylated fraction is then removed from the unmethylated fraction through gel purification of DNA fragments greater than 1kb.* The remaining nebulized DNA is subjected to the same gel purification scheme, but with no McrBC treatment. In a single hybridization, the untreated sample is labeled with Cy5 and the McrBC-treated sample with Cy3. Thus, after labeling and microarray hybridization, the ratio of normalized Cy5 to normalized Cy3 represents the relative methylation at the sequence represented by the spot on the microarray. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively. ddm1 seedlings, 9 days old. The two samples in this series are complementary hybridizations in a dye-swap analysis. This is the normalized result of the paired dye swap samples VC131 and VC135. The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity. To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using both family-wise error rate (FWER) and false discovery rate (FDR) controlling methods. The step-down multiple comparisons procedure of Holm (1979) was used to control the FWER below alpha = 0.01, while the step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent. Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the last two columns. Keywords: other
2004-06-12 | GSE1330 | GEO
Project description:A set of 5,908 69-70 mers oligonucleotides that correspond to all C. glabrata putative open reading frames and some non-coding sequences was designed and synthesized at Pasteur Institute, France. Each oilgonucleotide was dissolved into 50% DMSO and spotted on UltraGAPsTM glass slides (Corning Incorporated, Acton, MA) in duplicate to generate whole genome microarray for C. glabrata. The microarray was printed at Biotechnology Research Institute/National Research Council of Canada in Montreal. The sequence information of the oligonucleotides and the micorarray setup can be found at platform GPL3922. Using the microarray, the transcriptional profiles of C. glabrata cells that were coincubated with J774A.1 murine Macrophage-like cells for 2 and 6 hrs were examined. At each time point, three biological repeats were done. 20 ug of total RNA from either macrophage-ingested C. glabrata cells (experimental sample) or the medium-alone controls (control sample) was used to synthesize Cy5- or Cy3-labeled cDNA probes with an anchor primer [(dT)18(dA/dG/dC)] in the presence of Cy5- or Cy3-dCTP (PerkinElmer). For each pair of experimental and control samples, dye-swap was performed, that is, two probe mixtures, the Cy5-experimental plus the Cy3-control probes, and conversely, the Cy3-experimental plus the Cy5-control probes were individually hybridized with a single C. glabrata microarray slide. The hybridization and subsequent washing conditions follows the instruction on the manual for UltraGAPsTM glass slides. The hybridized microarrays were scanned with Axon 4000B scanner, and Data were extracted using Axon GenePix program. Log2 (experimental/control) for each spot on the microarray was calculated. From each dye-swap experiment, the Log2 (experimental / control) for each spot were averaged. Finally, 6 Log2 (experimental/control) values (3 repeats × duplicate spots on each slide) were imported into SAM (significance analysis of microarrays) software for statistical analysis. For genes that are considered significantly induced or repressed, the median of false discovery rate (FDR) equals to 0, while the 90% FDR is less than 0.001. Keywords: transcriptional profiling by microarray
2006-10-19 | GSE6058 | GEO
Project description:Cy3-labeled cDNA from brains of neonatal C57BL Cx43 null, Cx43 heterozygous and Cx32 null mice were compared among themselves and to Cy3-labeled cDNA from brains of neonatal C57BL wildtype mice through Cy5-labeled sample reference prepared at once for the entire experiment from aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from adult male and female C57BL mice.
2004-11-12 | GSE1954 | GEO