Deletions_TETs_WTs
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE457 | GEO | 2003/06/12
SECONDARY ACCESSION(S): PRJNA85057
REPOSITORIES: GEO
Similar Datasets
Project description:Analysis of noncoding RNA processing phenotypes in mutant yeast strains, with isogenic wildtype strains as controls two-color microarrays, total RNA labeled directly with Alexa Ulysis 546 and 648 dyes, dye-swap, eight replicates of each oligo per slide, Lowess smoother, Hedge et al. 2002 protocols, see Peng, Robinson et al., 2003.
2003-06-11 | E-GEOD-457 | biostudies-arrayexpress
Project description:Congestive heart failure was done by artificial myocardial infarction. After extracting total RNA from control and infarcted ventricles with Triazol, messenger RNA was isolated with Qiagen mRNA isolation kit. About 1.5ug poly A+ RNA was taken for probe preparation. Probe was labeled with Alexa Fluor 546 and 657. Labeled probes were hybridized with Qiagen rat unigene oligo library. After 2 low and 1 high stringency washes Prolong Antifade was added to the slides to prevent bleaching effect. The data ratio was normalized using a location and intensity dependent Lowess formula. Keywords: other
2003-09-08 | GSE632 | GEO
Project description:Congestive heart failure was done by artificial myocardial infarction. After extracting total RNA from control and infarcted ventricles with Triazol, messenger RNA was isolated with Qiagen mRNA isolation kit. About 1.5ug poly A+ RNA was taken for probe preparation. Probe was labeled with Alexa Fluor 546 and 657. Labeled probes were hybridized with Qiagen rat unigene oligo library. After 2 low and 1 high stringency washes Prolong Antifade was added to the slides to prevent bleaching effect. The data ratio was normalized using a location and intensity dependent Lowess formula.
2010-06-05 | E-GEOD-632 | biostudies-arrayexpress
Project description:adt12-01_uprt - plant rabt n°1 - Impact of RNA labeling by Plant RABT on plant transcriptome - Determine the incidence of RNA marking by the RABT method Plantation on the plants transcriptome. In several studies Clearly et al. have described a method referred as "4TU tagging" which can be use to study mRNA synthesis and decay either in a mixed population of cells or in a specific cell type (Cleary, Meiering et al. 2005, Zeiner, Cleary et al. 2008, Miller, Robinson et al. 2009, Rabani et al., 2011). Through the specific cell type expression in drosophila and mammalian cells of theToxoplasma gondii uracil PhosphoribosylTransferase activity and the metabolization of the uracil analog 4-thiouracil (4 TU), mRNA were selectively tagged, purified and used in microarray based analysis.
2014-09-10 | GSE60532 | GEO
Project description:454 dataset for Hosia, et al. Torstensson et al. Dinasquet et al.
| PRJEB7907 | ENA
Project description:Leishmania are protists (class: Kinetoplastida) with a single multifunctional flagellum, which forms a canonical motile 9+2 microtubule axoneme in the promastigote forms. Deletion of gene CFAP44 (LmxM.14.1430) caused a reduction in promastigote motility (Beneke et al., PLoS Pathogens, 2019; accepted). To study the changes in protein composition in CFAP44 deficient axonemes, flagellar skeletons were isolated from CFAP44 knockout mutants and the parental cell line L. mex Cas9 T7 (Beneke et al., R Soc Open Sci. 2017; 4(5):170095) using a modified version of the method by Robinson et al., (Methods Enzymol. 1991; 196:285-99). Liquid chromatography tandem mass spectrometry and a label-free quantitation method (SINQ; Trudgian et al., 2011, Proteomics 10.1002) were used to identify proteins enriched in each fraction. This PRIDE upload contains .RAW and .XML files, as well as the SINQ quantification output file “SINQ_raw_data”. XML files are named SUB9810; MSS11680. .RAW files are structured as follows: “CFAP44 mutants: Qex01_SVH_180422_TomBeneke_B29_F_001”; “Cas9 T7 parentals: Qex01_SVH_180422_TomBeneke_Cas9_F_005”.
2020-01-20 | PXD014077 | Pride
Project description:Preparation of sequencing libraries and sequencing analysis using Illumina HiSeq 3000 platform (50 bp single-read module) were conducted at the Genomics Core of UT Health San Antonio. Sequencing reads were preprocessed by Trim Sequences tools in CLC Genomics workbench. Remaining reads were then aligned to mouse GRCm38(mm10) reference genome using RNA-Seq Analysis module in CLC Genomics workbench. To determine differentially expressed genes, exact test were performed after filtering lowly expressed gene (counts per million < 1 in more than three samples across the dataset) using edgeR package (Robinson, McCarthy et al. 2010). Gene Ontology (GO) analysis were performed using DAVID (Dennis, Sherman et al. 2003) and then visualized by GOplot (Walter, Sanchez-Cabo et al. 2015).
2020-04-16 | GSE133140 | GEO
Project description:Rat ventricular cardiomyocytes were prepared from 18 day old fetus. Approximately 6 million cells were plated on 100 mm culture plate. The serum used in the medium was depleted from thyroid hormone by passing through anion exchange resin column. After 48 hours of growth with 70% confluency, cells were exposed to either T3, DITPA or CGS for another 48 hours before harvesting. Final concentrations of T3, DITPA and CGS in the medium were 6nM, 218nM and 1nM respectively. RNA was prepared from cells with Triazol. Twenty micrograms of total RNA was reverse transcribed and labeled with Alexa Fluor 546 and 647. Labeled probes were hybridized with Qiagen's rat unigene oligo library. After 2 low and 1 high stringency washes Prolong antifade was added to the slides to prevent bleaching effect. Slides were scanned in Array Worx scanner with dual wave length. The data ratio was normalized using a location and intensity dependent Lowess formula. Keywords: equivalent probe
2003-08-23 | GSE602 | GEO
Project description:adt12-01_uprt - plant rabt n°1 - Impact of RNA labeling by Plant RABT on plant transcriptome - Determine the incidence of RNA marking by the RABT method Plantation on the plants transcriptome. In several studies Clearly et al. have described a method referred as "4TU tagging" which can be use to study mRNA synthesis and decay either in a mixed population of cells or in a specific cell type (Cleary, Meiering et al. 2005, Zeiner, Cleary et al. 2008, Miller, Robinson et al. 2009, Rabani et al., 2011). Through the specific cell type expression in drosophila and mammalian cells of theToxoplasma gondii uracil PhosphoribosylTransferase activity and the metabolization of the uracil analog 4-thiouracil (4 TU), mRNA were selectively tagged, purified and used in microarray based analysis. 6 dye-swap - treated vs untreated comparison
2014-09-10 | E-GEOD-60532 | biostudies-arrayexpress