Margalefidinium polykrikoides
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ABSTRACT:
PROVIDER: PRJNA662012 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification This experiment is part of a much larger experiment. We have produced 4 454 metatranscriptomic datasets and 6 454 metagenomic datasets. These were derived from 4 samples. The experiment is an ocean acidification mesocosm set up in a Norwegian Fjord in 2006. We suspended 6 bags containing 11,000 L of sea water in a Coastal Fjord and then we bubbled CO2 through three of these bags to simulate ocean acidification conditions in the year 2100. The other three bags were bubbled with air. We then induced a phytoplankton bloom in all six bags and took measurements and performed analyses of phytoplankton, bacterioplankton and physiochemical characteristics over a 22 day period. We took water samples from the peak of the phytoplankton bloom and following the decline of the phytoplankton bloom to analyses using 454 metagenomics and 454 metatranscriptomics. Day 1, High CO2 Bag and Day 1, Present Day Bag, refer to the metatranscriptomes from the peak of the bloom. Day 2, High CO2 Bag and Day 2, Present Day Bag, refer to the metatranscriptomes following the decline of the bloom. Obviously High CO2 refers to the ocean acidification mesocosm and Present Day refers to the control mesocosm. Raw data for both the metagenomic and metatranscriptomic components are available at NCBI's Short Read Archive at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000101
2008-02-08 | E-GEOD-10119 | biostudies-arrayexpress
Project description:Dynamics of Microbial community compositions in Cochlodinium polykrikoides bloom and non-bloom period Metagenome
| PRJNA530338 | ENA
Project description:To identify the transcripome of dinoflagellate Cochlodinium polykrikoides that responded to algicide copper sulfate
2017-02-10 | GSE75463 | GEO
Project description:The purpose of this study was to quantify the effects of basal leaf removal applied in Sangiovese cultivar at two different phonological stages, pre-bloom and veraison, on berry composition. As very few papers were published about the regulation of gene expression induced by vineyard management techniques, we report the first global transcriptomic analysis (integrated with agronomic and biochemical data) aiming to determine the molecular mechanisms that control Sangiovese berry composition. The comparison of gene expression profiles of defoliated vines at pre-bloom and at veraison with the control, revealed a common transcriptional response at the end of veraison in both treated berries, but also a more extensive transcriptome rearrangement in pre-bloom defoliated ones, which could be linked to the strong biochemical changes detected in the berry after pre-bloom veraison.
2013-03-08 | GSE40487 | GEO
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification
2008-02-08 | GSE10119 | GEO
Project description:Cucumber (Cucumis sativus L.) is an economically important vegetable cultivated all over the world. Grafting can produce bloomless or sparse-bloom cucumber, which is welcomed by increasing consumers. Bloom granule is tine glandular hair, which is hard and rare studied on its formation and related genes. Mutifunctional RNA-seq is a recently developed analytical approach for transcriptome profiling via high-throughput sequencing and has been recently applied to a wide variety of organisms, which provide us reliable technical means detect bloom formation and related genes. In this study, we chose a cucumber inbred line (Shannong No.5) and two pumpkin rootstock lines as materials, and constructed four tested cucumbers, grew plants in “Yamazaki cucumber nutrient solution formula” prepared by deionized water, treated plants with or without 1.7mM potassium silicate 2 hours before collecting pericarp. Each treatment were duplicated twice.16 cDNA libraries were constructed from pericarp of a cucumber inbred line (own-rooted cucumber), C/C (self-grafted cucumber), M/C (More bloom, cucumber grafted onto “3225” rootstock) and L/C(Less bloom, cucumber grafted onto “3212” rootstock). We obtained 17,215,769~17,529,047 high quality reads, and 18,804~19,358 genes from each sample. All reads can be mapped to the cucumber genome (Version 2). By RPKM comparing, we got 38 comparing combinations with differentially expressed genes (DEGs), obtained 38 significantly expressed combinations by FDR≤0.001 and the absolute value of log2Ratio≥1 as the thresholds. These results suggest that there are many differences and genes expression mode among effects of grafting or added silicon. This study addresses a preliminary analysis and offers a foundation for future genomic research in the bloom formation of cucumber.
2020-04-02 | GSE79829 | GEO
Project description:The purpose of this study was to quantify the effects of basal leaf removal applied in Sangiovese cultivar at two different phonological stages, pre-bloom and veraison, on berry composition. As very few papers were published about the regulation of gene expression induced by vineyard management techniques, we report the first global transcriptomic analysis (integrated with agronomic and biochemical data) aiming to determine the molecular mechanisms that control Sangiovese berry composition. The comparison of gene expression profiles of defoliated vines at pre-bloom and at veraison with the control, revealed a common transcriptional response at the end of veraison in both treated berries, but also a more extensive transcriptome rearrangement in pre-bloom defoliated ones, which could be linked to the strong biochemical changes detected in the berry after pre-bloom veraison. Total RNA recovered from a pool of berries derived from three control plants (C) was compared to total RNA from a pool of berries derived from three defoliated vines at pre-bloom (PB, JD 147,6 basal leaves and relative laterals removed from each shoot) and three defoliated vines at veraison (V, JD 211,6 basal leaves and relative laterals removed from each shoot) at beginning of veraison (BV), end of veraison (EV) and harvest (H). For each sampling date microarray analyses were conducted for three different biological replicates for treatment.
2013-03-08 | E-GEOD-40487 | biostudies-arrayexpress