biostudies-arrayexpresssanjay khadayateSchizosaccharomyces pombehttps://www.ebi.ac.uk/biostudies/studies/E-TABM-843Here we used DNA microarrays to identify hyperadenylated transcripts detected in pab2 cells. Using this genome-wide approach, we found that the absence of Pab2 leads to the accumulation of polyadenylated snoRNAs and we describe the molecular mechanism of their accumulation.biostudies-arrayexpressSample Processing - Cells were transformed with PCR products by the lithium acetate method. All gene disruptions were performed by PCR-mediated gene targeting (Bahler et al., 1998) using 100-nt oligonucleotides with 80-nt from the appropriate regions of the genomic sequences to be targeted. The oligonucleotide sequences used for the construction of these strains are available upon request. All gene knockouts were confirmed by RT-PCRHybridization - Hybridization was performed at 49°C in a buffer containing 48% formamide using LifterSlips (Erie Scientific) and a hybridisation oven with humid chamber (Boekel Scientific)Nucleic Acid Extraction - Total RNA was isolated from S. pombe cells using a hot phenol method followed by phenol-chloroform extractions, precipitation, and purification using Qiagen RNeasy columnsGrowth Protocol - S. pombe was grown at 30°C in yeast extract medium with amino acid supplements (YES).Labeling - To generate fluorescently labelled samples for microarray hybridisation, we used a direct labelling protocol. 10–20 microgram of total RNA was reverse transcribed into cDNA with Superscript enzyme (GibcoBRL) and an oligo-dT17 primer in the presence of Cy3- or Cy5-dCTP (PerkinElmer)MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataAdditional FilesMAGE-TAB FilesArray DesignsFeature Extraction - Microarrays were scanned using a GenePix 4000 B laser scanner, and fluorescence signals were analysed using GenePix Pro software (Axon Instruments). Array images that did not pass minimal quality thresholds were not used (median signal-to-background >3; median signal-to-noise >5;Assay Data Transformation - Normalization was done with in house script which discards data from spots with failed or faulty PCR products by masking them 'absent'. We use a script for data pre-processing . To filter out unreliable data, we only use signals from those spots with more than 50% of the pixels greater than two standard deviations (SD) above local background signal in both channels. Data from spots showing more than 95% of the pixels greater than 2 SD above local background in one channel are retained, even if the other channel does not pass the normal cutoffMetabolomicsUnknownTranscriptomicsGenomicsProteomicstranscription profiling by arraySchizosaccharomyces pombeThe Nuclear Poly(A)-Binding Protein Interacts with the Exosome to Promote Synthesis of Noncoding Small Nucleolar RNAsJean-François Lemay, Annie DAmours, Caroline Lemieux, Daniel H. Lackner, Valérie G. St-Sauveur, Jürg Bähler, François Bachandsanjay khadayatefalseTranscription profiling of fission yeast wild type and Pab2 knockout strains to invstigate the role of Pab2 in synthesis of noncoding snoRNAsHere we used DNA microarrays to identify hyperadenylated transcripts detected in pab2 cells. Using this genome-wide approach, we found that the absence of Pab2 leads to the accumulation of polyadenylated snoRNAs and we describe the molecular mechanism of their accumulation.2010-01-21T00:00:00Z2022-11-23T05:58:55.342Z2022-03-11T13:18:34.998ZE-TABM-843EFO_0002768