FissionNet
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ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe
PROVIDER: GSE74354 | GEO | 2015/12/31
SECONDARY ACCESSION(S): PRJNA299808
REPOSITORIES: GEO
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Project description:Splicing profiling of deletion strains compared to wild-type control 1 replicate for each WT/deletion comparison Splicing sensitive S. pombe microarrays (Agilent-027365) were used to compare the splicing profile of various deletion strains relative to wild-type. The ÎSPAC1952.06c strain displayed reduced growth at 37°C so to elicit a strong phenotype we shifted this strain and the WT reference sample prior to collecting cells
2015-12-31 | E-GEOD-74354 | biostudies-arrayexpress
Project description:Splicing profiling of deletion strains compared to wild-type control
2016-05-02 | GSE79153 | GEO
Project description:Transcriptional profiles of S. cerevisiae strains with deletions of mth1, std1, or both were compared to that of a wild-type strain during growth on synthetic complete media with galactose as the carbon source, with the intent to understand each protein's contribution to the cells' response to glucose. Single-condition experiment, mth1 delete, std1 delete or the double mth1/std1 deletion strain vs. a wild type yeast strain. Biological replicates: 2. Rep. 1: Independently isolated RNA preps for each mutant was compared against a single WT sample. Rep. 2: A second set of mutant and WT samples was used to repeat the profiling. Two replicate spots representing each gene are present per array.
2010-05-06 | E-GEOD-17437 | biostudies-arrayexpress
Project description:This project focused in the proteomic characterization of the secreted proteome of a Rv1002c (Protein mannosyltransferase) knock-out mutant and its wild type counterpart. The analysis was carried out using a M. tuberculosis ΔleuDΔpanCD auxotroph Rv1002c wild type compared to M. tuberculosis ΔleuDΔpanCDΔRv1002c. Both strains were grown in triplicate and their whole cell lysate (WCL) and secreted proteins (CFP) where purified, trypsin digested and characterized by liquid-chromatography coupled with tandem mass spectrometry (LC-MS/MS). Three replicate injections were performed for each of the sampels. The resulting spectra were searched against an M. tuberculosis database and relative protein abundance was determined using normalized spectral counts. Protein abundance differences were tested by Student’s t test. Abundance of 39 secreted proteins was significantly different between the WT and the ΔRv1002c. Decrease abundance of known glycoproteins, including several lipoglycoproteins was observed in the ΔRv1002c strain. In the WCL, 61 proteins presented significantly different abundance between the WT and the ΔRv1002c strains, including 4 proteins that were completely absent in the mutant (Rv2510c, PknF, Mpt70 and CeoC).
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Project description:CD14+ Macrophage were challenged with Wildtype (WT), or S1154-deletion mutant (Del), and sequenced at timepoints zero hours (T0) and twenty-four hours (T24). To generate DEGs T0 and T24 timepoints were compared, a multifactor DESEQ2 run comparing T0 and T24 in both Wildtype and Deletion strains, and a direct comparison of T24 timepoints in Mutant and Deletion were generated.
2020-11-30 | GSE138793 | GEO
Project description:Dynamic control of gene expression is crucial for most aspects of cell physiology and at its core is RNA polymerase II (RNAPII). Using 53 RNAPII point mutants, we generated a point mutant epistatic miniarray profile (pE-MAP) comprising ~60,000 quantitative genetic interactions in Saccharomyces cerevisiae. This enabled functional assignment of RNAPII sub-domains, including connections to protein complexes. Using splicing microarrays and point mutants altering elongation rates in vitro, we found an inverse relationship between RNAPII speed and in vivo splicing efficiency. Furthermore, the pE-MAP classified groups of fast and slow mutants that favor upstream and downstream start site selection, respectively. Finally, the pE-MAP identified Sub1 as a positive transcription factor regulating start site selection and splicing. These data reveal striking coordination of polymerization rate with transcription initiation and splicing, suggesting transcription rate is tuned to coordinate multiple gene expression steps. The pE-MAP approach provides a powerful strategy to understand other multi-functional machines at amino acid resolution. Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used in one of the channels for each hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Using the Erlenmeyer growth protocol up to five deletion strains were grown on a single day. In the tecan platereader, up to eleven deletion strains could be grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance. Strains with point mutations in either rpb1, rpb2 or rpb7 subunits of RNA polymerase II (RNAPII) examined under normal growth conditions. The mutated RNAPII subunit is present on URA3 or LEU2 marked CEN plasmid, and the corresponding genomic RNAPII subunit deleted. Strains labeled as wildtype also have the relevant genomic RNAPII subunit deleted, but complemented with wildtype RNAPII subunit on CEN plasmid.
2013-08-06 | E-GEOD-47429 | biostudies-arrayexpress
Project description:This is parallel comparison of gene regulation by Gcn5 in evolutionarily divergent yeasts S. pombe and S. cerevisiae. Our study showed Gcn5 is required for a similar spectrum of stress responses in both organisms, including the response to KCl. This DNA microarray studies is to find conserved or diverged gene regulation pattern under KCl stress condition in the two yeasts. There are 6 subsets in total, 3 subsets in each evolutionarily divergent yeasts including the following: 1 gcn5 mutant compared to wt under rich medium without treatment, 2 gcn5 mutant compared to wild type both under KCl treatment, 3 wild type strains under KCl treatment compared to wild type without treatment. Keywords: stress response, Gcn5, Comparative genomics, Transcriptional co-activator
2010-01-01 | GSE5218 | GEO
Project description:A collection of budding yeast wild types grown in parallel to 1,484 budding yeast deletion mutants to assess day-to-day variance. Related to series GSE42526 and GSE42527. Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used in one of the channels for each hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Using the Erlenmeyer growth protocol up to five deletion strains were grown on a single day. In the tecan platereader, up to eleven deletion strains could be grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance.
2014-04-24 | E-GEOD-45115 | biostudies-arrayexpress
Project description:We report the profiling of induced mRNA transcripts in two C. elegan replicate populations -- WT (N2) and mutant strain with deficient HLH30. Both strains were fed either OP50 strain of e-coli (normal feed) or S. aureus
2015-06-04 | GSE57739 | GEO
Project description:This data set contains samples from Lactobacillus plantarum WCFS1 wild type and its CcpA mutant derivative. Both strains were grown in duplicate (samples L and R) and at four different growth stages samples were taken (early, mid and late log phase, early stationary phase). Samples were compared to each other within one strain and between the two strains. This allows the comparison of the wild type strain to its CcpA derivative in time. Further it allows comparison within one strain during different growth stages.
2010-09-10 | GSE24021 | GEO