GEO DataSets

(Submitter supplied) The filamentous diazotrophic cyanobacteria Trichodesmium spp. supply fixed nitrogen (N) to the N-depleted oligotrophic oceans where their growth is often limited by the low availability of phosphorus(P) and/or iron. Previous studies have mostly been focused on the effects of ocean acidification on Trichodesmium under nutrient sufficient or iron-limited conditions. Only a few studies have examined the impacts of ocean acidification on Trichodesmium grown at low P concentrations using non-steady-state batch cultures. more...

Organism:

Trichodesmium erythraeum IMS101

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23685

6 Samples

Download data: TXT

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

Organism:

Trichodesmium erythraeum IMS101

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL22446 GPL22441

23 Samples

Download data

(Submitter supplied) Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS) and RNA-Seq (i.e. transcriptomics) to examine the long-term epigenomic dynamics of an experimenta evolution study under high CO2 in the marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly change in response to short-term high CO2 exposure, which are then maintained for 4.5 years even after adaptation (i.e. more...

Organism:

Trichodesmium erythraeum IMS101

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL22441

19 Samples

Download data: TXT

(Submitter supplied) Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS) and RNA-Seq (i.e. transcriptomics) to examine the long-term epigenomic dynamics of an experimenta evolution study under high CO2 in the marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly change in response to short-term high CO2 exposure, which are then maintained for 4.5 years even after adaptation (i.e. more...

Organism:

Trichodesmium erythraeum IMS101

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22446

4 Samples

Download data: TXT

(Submitter supplied) We present population-level epigenetic variation in Trichodesmium erythraeum IMS101 associated with steady-state Fe-limitation at two different P concentrations on both short (i.e. 2 months) and long timescales (i.e. ~1 year).

Organism:

Trichodesmium erythraeum IMS101

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL23685

6 Samples

Download data: BED, TXT

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

Organism:

Trichodesmium; Trichodesmium erythraeum IMS101; Trichodesmium erythraeum 21-75; Trichodesmium thiebautii VI-1

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

5 related Platforms

15 Samples

Download data: TXT

(Submitter supplied) Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS), RNA-Seq (i.e. transcriptomics), high-CO2 physiology experiments, and spatiotemporally separated samples isolated in situ (i.e. directly from the ocean) to examine the metabolic potential of genome-wide cytosine (5mC) methylation (i.e. epigenomics), its potential impacts to transcriptional dynamics under both present-day and future ocean acidification conditions, and its biogeographic conservation in the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.

Organism:

Trichodesmium erythraeum IMS101

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22446

4 Samples

Download data: TXT

(Submitter supplied) Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS), RNA-Seq (i.e. transcriptomics), high-CO2 physiology experiments, and spatiotemporally separated samples isolated in situ (i.e. directly from the ocean) to examine the metabolic potential of genome-wide cytosine (5mC) methylation (i.e. epigenomics), its potential impacts to transcriptional dynamics under both present-day and future ocean acidification conditions, and its biogeographic conservation in the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.

Organism:

Trichodesmium; Trichodesmium erythraeum 21-75; Trichodesmium thiebautii VI-1; Trichodesmium erythraeum IMS101

Type:

Methylation profiling by high throughput sequencing

4 related Platforms

11 Samples

Download data: FA, TXT

(Submitter supplied) Our paper presents the results of a study in which we used Illumina RNA-Seq (i.e. transcriptomics) and high-CO2 nutrient limitation experiments to examine transcriptional variation of iron-limited, phosphorus-limited, and iron-phosphorus co-limited cultures following long-term (~7 years) low- (380 µatm CO2) and high-CO2 (750 µatm CO2) selection. Hence, we describe the molecular physiology of the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.

Organism:

Trichodesmium erythraeum IMS101

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22446

16 Samples

Download data: TXT

(Submitter supplied) Investigation of whole genome gene expression level changes in Trichodesmium erythraeum IMS101 during a 24-hr light and dark cycle. The diel gene expression analyzed in this study is further described in Muñoz-Marin, M., I. N. Shilova, T. Shi, H. Farnelid & J. P. Zehr. 2019. The transcriptional cycle is suited to daytime N2 fixation in the unicellular cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A). more...

Organism:

Trichodesmium erythraeum IMS101

Type:

Expression profiling by array

Platform:

GPL23571

28 Samples

Download data: CALLS, PAIR

(Submitter supplied) NimbleGen design name 080610_Trich_erth_UCSC_TS_expr, NimbleGen design ID 7738. A whole genome ORF-based expression design for 4788 genes from Trichodesmium erythraeum IMS101 with up to six 60-mer probes per gene, plus tiling of 60-mer probes at a 150-bp interval for intergenic regions >60bp in length. Each ORF-based probe is replicated 2 times. The design includes random GC and other control probes. more...

Organism:

Trichodesmium erythraeum IMS101

1 Series

28 Samples

Download data: NDF, NGD