GEO DataSets

(Submitter supplied) Prochlorococcus is found throughout the euphotic zone in the oligotrophic open ocean. Deep mixing and sinking in aggregates or while attached to particles can, however, transport cells below this sunlit zone, depriving them of light for extended periods of time and influencing their circulation via ocean currents. Viability of these cells over extended periods of darkness could shape the ecology and evolution of the Prochlorococcus collective. more...

Organism:

Alteromonas macleodii; Prochlorococcus marinus str. NATL2A

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34397

42 Samples

Download data: TSV

(Submitter supplied) Prochlorococcus is an obligate marine microorganism which are dominant autotroph in tropical and subtropical central oceans. However, what is the low salinity boundary and how Prochlorococcus would response to low salinity exposure is still unknown. In this study, we first tested the growing salinity range of two Prochlorococcus strains, NATL1A and MED4, and then compared the global transcriptome of their low salinity acclimated cells and cells growing in normal seawater salinity. more...

Organism:

Prochlorococcus marinus str. NATL1A; Prochlorococcus marinus subsp. pastoris str. CCMP1986

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL31902 GPL31900

12 Samples

Download data: TXT

(Submitter supplied) Examining the impact of short term exposure to HDPE and PVC plastic leachates on gene transcription in Prochlorococcus cultures in vitro

Organism:

Prochlorococcus marinus str. NATL2A; Prochlorococcus marinus str. MIT 9312

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25433 GPL25434

18 Samples

Download data: CSV

(Submitter supplied) We examine how the transcriptome of Prochlorococcus strain NATL2A changes in response to extended light deprivation, both when grown alone and in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002.

Organism:

Alteromonas macleodii; Prochlorococcus marinus str. NATL2A

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20970 GPL20972

113 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:

Prochlorococcus marinus str. NATL2A; Alteromonas macleodii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20972 GPL20970

42 Samples

Download data: TXT

(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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Prochlorococcus marinus str. NATL2A; Synechococcus phage syn9; Cyanophage P-TIM40; Parasynechococcus marenigrum WH 8102; Synechococcus sp. WH 8109; Synechococcus sp. WH 7803

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

4 related Platforms

187 Samples

Download data: CEL

(Submitter supplied) Cyanobacteria are highly abundant in the oceans and are constantly exposed to lytic viruses. The T4-like cyanomyoviruses are abundant in the marine environment and have broad host ranges relative to other cyanophages. It is currently unknown whether broad-host-range phages specifically tailor their infection program for each host, or employ the same program irrespective of the host infected. Also unknown is how different hosts respond to infection by the same phage. more...

Organism:

Prochlorococcus marinus str. NATL2A; Cyanophage P-TIM40; Parasynechococcus marenigrum WH 8102; Synechococcus sp. WH 8109; Synechococcus sp. WH 7803; Synechococcus phage syn9

Type:

Expression profiling by array

Platform:

GPL19456

133 Samples

Download data: CEL, TXT

(Submitter supplied) Carbon fixation plays a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus--—the most abundant phototroph in the oligotrophic oceans--—the carbon-concentrating mechanism (CCM) is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. more...

Organism:

Prochlorococcus marinus subsp. pastoris str. CCMP1986

Type:

Expression profiling by array

Platform:

GPL19747

40 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli; Shigella flexneri; Haemophilus influenzae; Staphylococcus aureus; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Human betaherpesvirus 6; human gammaherpesvirus 4; Human T-cell leukemia virus type I; Coxsackievirus A9; Human herpesvirus 4 type 2; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin; Betapolyomavirus macacae; Helicobacter pylori; Yersinia enterocolitica; Chlamydia trachomatis; Mycobacterium tuberculosis variant bovis; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Coxsackievirus B4; Coxsackievirus A20; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10; Proteus mirabilis; Streptococcus pyogenes; Mycobacterium gordonae; Trypanosoma cruzi; Caprine arthritis encephalitis virus; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Human adenovirus 12; Human endogenous retrovirus K; Human Endogenous Retrovirus IDDMK1,2-22; Torque teno virus; Prochlorococcus marinus str. MIT 9202; Human rotavirus MP409; Paraburkholderia fungorum; Staphylococcus aureus A9635; Hepacivirus hominis; Klebsiella pneumoniae; Porphyromonas gingivalis; Mycobacterium avium subsp. paratuberculosis; Mycobacterium tuberculosis; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Human herpesvirus 4 strain B95-8; Human immunodeficiency virus 1; Human herpesvirus 4 type 1; Coxsackievirus B4 (strain E2)

Type:

Protein profiling by protein array

Platforms:

GPL19700 GPL19692 GPL19701

29 Samples

Download data: XLSX

(Submitter supplied) The aim of the array was to determine the BXD2 mouse sera IgG and IgM reactivity profile to linear peptide epitopes. Pooled sera from three 6-9 month old BXD2 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens

Organism:

Chlamydia trachomatis; Streptococcus pyogenes; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis; Trypanosoma cruzi; Homo sapiens; Human herpesvirus 4 strain B95-8; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Coxsackievirus B4; Human adenovirus 12; Human Endogenous Retrovirus IDDMK1,2-22; Human rotavirus MP409; Hepacivirus hominis; Escherichia coli; Klebsiella pneumoniae; Proteus mirabilis; Porphyromonas gingivalis; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Mycobacterium gordonae; Mus musculus; Human betaherpesvirus 6; Human immunodeficiency virus 1; Human herpesvirus 4 type 2; Human herpesvirus 4 type 1; Human endogenous retrovirus K; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin; Haemophilus influenzae; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Coxsackievirus A9; Coxsackievirus B4 (strain E2); Betapolyomavirus macacae; Helicobacter pylori; Shigella flexneri; Yersinia enterocolitica; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Human T-cell leukemia virus type I; Coxsackievirus A20; Torque teno virus; Prochlorococcus marinus str. MIT 9202; Paraburkholderia fungorum; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10; Staphylococcus aureus A9635

Type:

Protein profiling by protein array

Platform:

GPL19701

2 Samples

Download data: XLSX

(Submitter supplied) The aim of the array was to determine the B6 mouse sera IgG and IgM reactivity profile to linear peptide epitopes. Pooled sera from three 6-9 month old B6 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens

Organism:

Chlamydia trachomatis; Streptococcus pyogenes; Mycobacterium tuberculosis variant bovis; Trypanosoma cruzi; Human betaherpesvirus 6; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Coxsackievirus B4; Human adenovirus 12; Human endogenous retrovirus K; Human Endogenous Retrovirus IDDMK1,2-22; Human rotavirus MP409; Hepacivirus hominis; Haemophilus influenzae; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Mycobacterium tuberculosis; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Human herpesvirus 4 strain B95-8; Human T-cell leukemia virus type I; Coxsackievirus A9; Prochlorococcus marinus str. MIT 9202; Coxsackievirus B4 (strain E2); Staphylococcus aureus A9635; Betapolyomavirus macacae; Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Mus musculus; Human immunodeficiency virus 1; Human herpesvirus 4 type 2; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin; Helicobacter pylori; Proteus mirabilis; Yersinia enterocolitica; Porphyromonas gingivalis; Mycobacterium gordonae; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Human herpesvirus 4 type 1; Coxsackievirus A20; Torque teno virus; Paraburkholderia fungorum; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10

Type:

Protein profiling by protein array

Platform:

GPL19701

2 Samples

Download data: XLSX

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

Type:

Expression profiling by array

Platform:

GPL8853

5 Samples

Download data: CEL, 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:

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

Type:

Expression profiling by array

Platform:

GPL11412

39 Samples

Download data: CEL

(Submitter supplied) To gain improved temporal, spatial and phylogenetic resolution of marine microbial communities, in this study we expanded the original prototype genome proxy array (an oligonucleotide microarray targeting marine microbial genome fragments and genomes), evaluated it against metagenomic sequencing, and applied it to time series samples from the Monterey Bay long term ecological research site. The expanded array targeted 268 microbial genotypes (vs. more...

Organism:

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

Type:

Other

Platform:

GPL10357

58 Samples

Download data: GPR

(Submitter supplied) RNA decay was measured in Prochlorococcus after inhibition of transcription by rifampicin using customized Affymetrix gene expression arrays. RNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome RNA stability of Prochlorococcus, a relatively slow-growing marine cyanobacterium doubling approximately once a day, which is extremely abundant in the oceans. 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:

GPL8853

20 Samples

Download data: CEL

(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:

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; Prochlorococcus marinus str. MIT 9313; Prochlorococcus marinus str. MIT 9515; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07; uncultured marine group II euryarchaeote 37F11; uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome; 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

Type:

Other

Platform:

GPL6012

28 Samples

Download data: GPR

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

Type:

Expression profiling by array

Platform:

GPL5471

45 Samples

Download data: CEL