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Next Generation Sequencing Analysis of Saccharopolyspora erytharea transcriptomes

ABSTRACT: We report the high-throughput profiling of saccharopolyspora erythraea life cycle in bioreactors. RNA was harvested at seven time-points from bioreactors, three points immediately before, one during and three following the metabolic switch (as evidenced by biomass cell dry weight). We prepared unstranded RNA libraries and sequenced 363 million reads for a total of 32.7Gb and a mean ~4,000 fold coverage of the genome. Our comprehensive sequencing showed the S.erythraea genome to be prevalently transcribed, with at least 85.8% of genome sequence from either strand being transcribed.

ORGANISM(S): Saccharopolyspora erythraea

PROVIDER: GSE39722 | GEO | 2013/06/18

SECONDARY ACCESSION(S): PRJNA171549

REPOSITORIES: GEO

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Next Generation Sequencing Analysis of Saccharopolyspora erytharea transcriptomes

Project description:We report the high-throughput profiling of saccharopolyspora erythraea life cycle in bioreactors. RNA was harvested at seven time-points from bioreactors, three points immediately before, one during and three following the metabolic switch (as evidenced by biomass cell dry weight). We prepared unstranded RNA libraries and sequenced 363 million reads for a total of 32.7Gb and a mean ~4,000 fold coverage of the genome. Our comprehensive sequencing showed the S.erythraea genome to be prevalently transcribed, with at least 85.8% of genome sequence from either strand being transcribed. We sequenced a bioreactor fermentation at seven time points.

2013-06-18 | E-GEOD-39722 | biostudies-arrayexpress

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2014-04-15 | E-GEOD-56541 | biostudies-arrayexpress

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Lysine succinylation in Saccharopolyspora erythraea

Project description:We identified a total of 5531 succinylated sites on 1654 proteins in Saccharopolyspora erythraea

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Complete Gene Expression Profiling of Saccharopolyspora erythraea NRRL 2338

Project description:A DNA microarray was designed and constructed using the genome sequence of Saccharopolyspora erythraea strain NRRL 2338. Following growth in liquid medium, we analysed the expression of 6494 ORFs along the time course. The results indicated that the 404 genes, whose expression significatively correlated with the time course, identify three distinct growth phases: a rapid growth until 32 h (phase A); a growth slowdown until 52 h (phase B); another rapid growth phase from 56 h to 72 h (phase C) before entering the stationary phase. We experimentally determined regional organization of transcription along the chromosome, highlighting differences between core and non-core regions, but also strand specific patterns of expression, and the behavior of major functional classes. Temporal expression of all the gene clusters for secondary metabolism was analyzed, confirming ery cluster up-regulation during the first growth phase, and finding out six secondary metabolism clusters that are clearly regulated during growth. The use of a DNA microarray, specifically designed on the Sac. erythraea genome sequence, improved specificity and sensitivity of gene expression analysis, giving a global and at the same time detailed picture of how Sac. erythraea genes are modulated. Keywords: time course

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