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Ume6D_BY4741 on expression/splicing microarrays

ABSTRACT: ume6D_BY4741 vegetative RNA compared to WT_BY4741 vegetative RNA. ume6D haploid was generated in the BY4741 strain background (ATCC: 201388) by PCR-mediated cassette-based gene replacement where the UME6 ORF was replaced with KANMX6, the deletion was verified by PCR.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE24680 | GEO | 2011/04/05

SECONDARY ACCESSION(S): PRJNA133625

REPOSITORIES: GEO

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ume6D_BY4741 on expression/splicing microarrays

Project description:ume6D_BY4741 vegetative RNA compared to WT_BY4741 vegetative RNA. ume6D haploid was generated in the BY4741 strain background (ATCC: 201388) by PCR-mediated cassette-based gene replacement where the UME6 ORF was replaced with KANMX6, the deletion was verified by PCR. Vegetatively grown; Dye swap; Reference vegetative WT_BY4741

2011-04-05 | E-GEOD-24680 | biostudies-arrayexpress

mer1D_SK1 meiotic time course on expression/splicing microarrays

Project description:Synchronized mer1D_SK1 meiotic time course. mer1D diploid was generated in the SK1 strain background (ATCC: MYA-2089) by PCR-mediated cassette-based gene replacement where the MER1 ORF was replaced with HIS3 from S. kluyveri then the transformants were sporulated and the homozygous deletion was verified by PCR.

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mer1D_SK1, mer2D_SK1, mer3D_SK1, spo22D_SK1, and spo70D_SK1 on expression/splicing microarrays

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Ume6 regulon

Project description:The Ume6 transcription factor in yeast is known to both repress and activate expression of diverse genes during mitotic growth and meiotic development. To obtain a more complete profile of the functions regulated by this protein, microarray analysis was used to examine transcription in wild type and ume6-deleted diploids during vegetative growth in glucose and acetate. Keywords = yeast Keywords = meiosis Keywords = sporulation Keywords = UME6 Keywords = micorarrays Keywords = GeneChips Keywords = bioinformatics Keywords: other

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Transcription profiling of Geobacter sulfurreducens wild type and pilR mutants with acetate as the electron donor and ferric citrate as the electron acceptor

Project description:G. sulfurreducens wild type and pilR mutant (GSU1495) were grown in chemostats for RNA extraction used for microarray analysis and qRT-PCR. The electron donor (acetate 5mM) was limiting at a dilution rate of 0.05 h-1 and ferric citrate(55mM) was used as the electron acceptor at 30C, as previously described (Esteve-Nunez et al., 2005). Analysis of acetate, Fe(II) and protein were performed as previously described (Esteve-Nunez et al., 2005). Disruption of the pilR gene (GSU1495) was made in G. sulfurreducens strain DL1 (ATCC 51573) by the recombinant PCR and single-step recombination method (Murphy et al., 2000), essentially as described (Lloyd et al., 2003). To disrupt the pilR gene a 2.25 kb DNA fragment was constructed by PCR in which 0.39 kb of the pilR coding sequence (codons 192 - 323) were replaced with the kanamycin resistance cassette (Knr) of pBBR1MCS-2 (Kovach et al., 1995). This fragment consisted of 29 bp of upstream sequence together with the first 575 bp of the pilR gene, followed by the kanr cassette (1.1 kb), and the last 409 bp of the pilR gene and 132 bp of downstream sequence. The mutant was selected in NBAF plates supplemented with kanamycin and incubated at 30C in an anaerobic chamber containing a mixture of 7% H2, 10% CO2, 83% N2. A single kanamycin-resistant colony was selected, tested for the insertion of the Knr cassette by PCR, and designated DLJK3.

2007-11-10 | E-JCVI-1 | biostudies-arrayexpress

Map1p overexpression versus control cells microarrays

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General retardation of mRNA degradation caused by speB 5’ UTR partial deletion in Streptococcus pyogenes

Project description:The speB gene of Streptococcus pyogenes has a long 5' UTR with unknown functions. Preliminary studies showed that the partial mutation of this region led to altered expression patterns of the speB gene and ropB, its upstream gene. In this study, we used microarray to examine the effect of speB 5' UTR mutation on the S. pyogenes transcriptome. The speB ORF and a large portion of the speB 5’ UTR (-1 to -527 from ATG) was replaced with an erythromycin resistant cassette gene (ermAM) to generate a ΔIG mutant. Transcriptome profiles of the wild-type (WT) and ΔIG mutant in the mid-exponential phase and early stationary phase (ST) were examined with microarray analysis.

2015-09-10 | E-GEOD-72838 | biostudies-arrayexpress

Expression analysis of DamP mRNAs using expressed molecular barcodes

Project description:We have generated 979 yeast strains in which the natural 3' UTR of essential gene mRNAs has been replaced by the same long 1.4 kb artificial 3' UTR (DAmP modification). Nonsense mediated mRNA decay (NMD) of these mRNA reporters was tested by using Agilent barcode microarrays by taking advantage of molecular barcodes introduced just downstream the stop codon during strain construction. We introduced in each DAmP strain either a neutral mutation (deletion of YEL068C) or the deletion of essential factors for NMD: NAM7 and NMD2. The resulting haploid cells were tested for changes in DAmP mRNA levels by comparing an RNA sample with a DNA genomic sample. Differences between the samples indicate the sensibility of the DAmP mRNAs to degradation through NMD. The large scale results were validated by Q-PCR analysis of individual strains. A strong negative correlation between the level of destabilization elicited by a long 3' UTR and the size of the coding sequence suggests that long ORF mRNAs can escape NMD even in the presence of a long 3' UTR.

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