Unknown,Transcriptomics,Genomics,Proteomics

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RNA-Seq of Saccharomyces cerevisiae cells carrying different YRR1 alleles in response to 4-nitroquinoline-N-oxide (4NQO) and to glycerol as the sole carbon source

ABSTRACT: In this study, we constructed three isogenic strains of S96 yrr1Î? background (its native YRR1 gene was knocked out) carrying three different YRR1 alleles, YRR1_S96, YRR1_YJM789 and YRR1_S96-I775E, respectively. We then conducted RNA deep sequencing (RNA-Seq) on the three strains grown in Yeast Peptone Dextrose medium (YPD), YPD + 4NQO and Yeast Peptone glycerol medium (YPglycerol). RNA-Seq was performed in biological duplicates on S96 cells carrying three different YRR1 alleles grown in YPD, YPD + 4NQO, YPglycerol

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Xiaoqing Rong-Mullins

PROVIDER: E-GEOD-74642 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: The carpel margin meristem is a vital multi-potent structure located in the medial domain of the Arabidopsis thaliana gynoecium, the female floral reproductive organ. The carpel margin meristem generates ovules that upon fertilization become seeds. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present an analysis of the transcriptional profile of the medial domain of the Arabidopsis gynoecium highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development. Results: Using a floral synchronization system and a SHATTERPROOF2 domain-specific reporter construct, paired with fluorescence-activated cell sorting, we assayed the transcriptome of the gynoecial medial domain with temporal and spatial precision. Our analysis reveals a set of genes that are differentially-expressed within the SHATTERPROOF2 expression domain that marks portions of the developing medial domain. Many members of this gene set have been shown previously to function during the development of medial domain-derived structures, including the ovules, thus validating our approach. Other uncharacterized members of this gene set, including a set of differentially-expressed cis-natural antisense transcripts, are potential novel regulators of medial domain development and candidates for future functional studies. Several members of the REM family of transcriptional regulators were enriched in the SHP2-expressing cell population including a previously unrecognized REM family member (At5g60142). Analysis of the abundance of specific transcriptional isoforms identified genes that may exhibit âisoform switchingâ behavior during gynoecial development. Conclusions: This data set provides genome-wide transcriptional insight into the development of the gynoecial medial domain that contains the carpel margin meristem, an important reproductive structure that gives rise to the ovules in Arabidopsis thaliana. Four samples (YFP-positive, YFP-negative, all-sorted, and non-sorted). Four biological replicates of each sample (except YFP-positive, collected in triplicated). Strand-specific libraries were sequenced (single-end) in two lanes of a HiSeq 2500 Illumina flow cell (each lane was later analyzed as a technical replicate).

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RNA-Seq of Saccharomyces cerevisiae cells carrying different YRR1 alleles in response to 4-nitroquinoline-N-oxide (4NQO) and to glycerol as the sole carbon source

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