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Nucleotide-resolution, genome-wide, 5'-end maps of the transcriptome of Propionibacterium acnes (cultured with and without potassium downshift)

ABSTRACT: The differential RNA-seq data contained within this entry is complemented by global RNA-seq and microarray data, which is also deposited in GEO. Duplicate cultures of Propionibacterium acnes strain KPA171202 were grown exponentially in batch culture under anaerobic growth. Samples were taken following subculture with and without potassium downshift (i.e. removal from medium). This produced 4 samples; 2 replicates x 2 conditions. Aliquots of each of the 4 samples were then incubated with or without incubation TAP (tobacco acid pyrophosphatase) before library construction. Thus, 8 libraries were analysed. TAP treatment allows the cloning and sequencing of 5' ends that were originally triphosphorylated.

ORGANISM(S): Propionibacterium acnes KPA171202

SUBMITTER: David Romero A.

PROVIDER: E-GEOD-46810 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Nucleotide-resolution, genome-wide transcriptome maps of Propionibacterium acnes (cultured with and without potassium downshift)

Project description:This data contained within this entry was produced as part of a study that included differential RNA-sequencing and microarray analysis. The results of the latter two have also been deposited in GEO Duplicate cultures of Propionibacterium acnes strain KPA171202 were grown exponentially in Holland Synthetic Medium (Holland et al.1979. J Appl Bacteriol 47: 383), which supports reproducible anaerobic growth. Samples were taken following subculture with and without potassium downshift (i.e. removal from medium).

2013-05-15 | E-GEOD-46883 | biostudies-arrayexpress

Comparison of nucleotide-resolution, genome-wide transcriptome maps of Escherichia coli K12 strain BW25113 and Streptomyces coelicolor A3(2) strain M145.

Project description:This data contained within this entry was produced as part of a study that included differential RNA-sequencing. S. coelicolor and E. coli reference strains were grown in batch culture with shaking. The E. coli sample was extracted during mid-exponential growth, while the S. coelicolor sample was extracted at the start of pigmented antibiotic production.

2013-04-20 | E-GEOD-46232 | biostudies-arrayexpress

Comparison of the nucleotide-resolution, genome-wide, 5'-end maps of the transcriptomes of Escherichia coli K12 strain BW25113 and Streptomyces coelicolor A3(2) strain M145

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2013-05-01 | E-GEOD-46507 | biostudies-arrayexpress

Candida glabrata transcription profile when grown under Niacin starvation or in human urine

Project description:The transcription profile of Candida glabrata grown under two different Niacin limitation conditions were determined. Condition 1 is comparing log phase C. glabrata cells (O.D. 0.5-0.6) grown in synthetic medium containing 0.016 uM versus 3.25 uM nicotinic acid (NA), a common form of Niacin. The NA concentration of 3.25 uM is the standard concentration in synthetic complete (SC) medium. Condition 2 is comparing log phase C. glabrata cells (O.D. 0.4-0.6) grown in 3 individual human urine samples (supplemented with 2% glucose) versus in SC medium. Keywords: transcriptional profiling by microarray GSM151863, GSM151869 are dye-swap experiment #1 and GSM151880, GSM151881 are dye-swap experiment #2 for Niacin limitation condition 1. GSM151934, GSM152116 are dye-swap experiment #1, GSM152118, GSM152119 are dye-swap experiment #2 and GSM152130, GSM152131 are dye-swap experiment #3 for Niacin limitation condition 2.

2010-06-05 | E-GEOD-6582 | biostudies-arrayexpress

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Investigation of Role of Eleven TonB Homologs in Carbohydrate Utilization by Bacteroides thetaiotaomicron

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2024-01-26 | PXD041518 | Pride

The transcriptome of erythromycin-resistant Campylobacter jejuni strain selected from NCTC 11168

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