GEO DataSets

(Submitter supplied) RNA-Seq technique was used to obtain the transcriptome map of Prochlorococcus MED4, including operons, untranslated regions, non-coding RNAs, and novel genes. Genome-wide expression profiles revealed that three factors contribute to core genome stabilization. First, a negative correlation between gene expression levels and protein evolutionary rates was observed. Highly expressed genes were overrepresented in the core genome but not in the flexible genome. more...

Organism:

Prochlorococcus marinus subsp. pastoris str. CCMP1986

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17528

10 Samples

Download data: TXT

(Submitter supplied) Prochlorococcus contributes significantly to ocean primary productivity. The link between primary productivity and iron in specific ocean regions is well established and iron limitation of Prochlorococcus cell division rates in these regions has been shown. However, the extent of ecotypic variation in iron metabolism among Prochlorococcus and the molecular basis for differences is not understood. Here, we examine the growth and transcriptional response of Prochlorococcus strains, MED4 and MIT9313, to changing iron concentrations. more...

Organism:

Tiamatvirus PSSP7; Prochlorococcus marinus str. MIT 9313; Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus phage P-SSM4

Type:

Expression profiling by array

Platform:

GPL11412

39 Samples

Download data: CEL

(Submitter supplied) Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present the comprehensive comparison of the structure and composition of the transcriptomes of two closely related Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We used large-scale strand-specific cDNA sequencing, microarray RNA profiling and computational analyses to characterize the transcriptomes of Prochlorococcus sp. more...

Organism:

Prochlorococcus marinus subsp. pastoris str. CCMP1986; Tiamatvirus PSSP7; Prochlorococcus phage P-SSM4; Prochlorococcus marinus str. MIT 9313

Type:

Expression profiling by array

Platform:

GPL8853

5 Samples

Download data: CEL, TXT

(Submitter supplied) We used microarray analysis to investigate whole genome transcriptome dynamics of the marine cyanobacterium Prochlorococcus sp. strain MED4 and the T7-like podovirus P-SSP7 over a time course during the 8 hour latent period of lytic infection prior to cell lysis. Manuscript Summary: Interactions between bacterial hosts and their viruses (phages) lead to reciprocal genome evolution through a dynamic co-evolutionary process1-5. more...

Organism:

Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus phage P-SSM4; Tiamatvirus PSSP7; Prochlorococcus marinus str. MIT 9313

Type:

Expression profiling by array

Platform:

GPL5471

45 Samples

Download data: CEL

(Submitter supplied) We report the full transcriptome of T4-like cyanophage P-HM2 infecting Prochlorococcus in light and dark

Organism:

Prochlorococcus phage P-HM2; Prochlorococcus marinus subsp. pastoris str. CCMP1986

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21611

40 Samples

Download data: TXT

(Submitter supplied) We examine how the transcriptome of Prochlorococcus strain NATL2A changes in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002. Significant changes in the Prochlorococcus transcriptome were evident within six hours of co-culture, with groups of transcripts changing in different temporal waves. Many transcriptional changes persisted throughout the 48-hour experiment, indicating that the presence of the heterotroph affected a stable shift in Prochlorococcus physiology. more...

Organism:

Alteromonas macleodii; Prochlorococcus marinus str. NATL2A

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20970 GPL20972

42 Samples

Download data: TXT

(Submitter supplied) Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a “genome proxy” microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. more...

Organism:

Prochlorococcus marinus str. MIT 9313; Prochlorococcus marinus str. MIT 9515; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07; uncultured marine alpha proteobacterium; uncultured Pseudomonadota bacterium; uncultured crenarchaeote 74A4; uncultured proteobacterium 65D09; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine bacterium EB000_55B11; uncultured crenarchaeote 4B7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus marinus str. MIT 9312; uncultured marine gamma proteobacterium EBAC31A08; uncultured marine bacterium EB0_41B09; uncultured proteobacterium 60D04; uncultured marine group II euryarchaeote 37F11; uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome

Type:

Other

Platform:

GPL6012

28 Samples

Download data: GPR

(Submitter supplied) We used the RNA-seq technology to do a genome-wide transcriptional analysis of A. pleuropneumoniae strain JL03 and investigated the transcriptome structure at a single-nucleotide resolution.The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures).

Organism:

Actinobacillus pleuropneumoniae serovar 3 str. JL03

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20603

1 Sample

Download data: BED