Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

Metatranscriptomes of phytoplankton blooms from an ocean acidification mesocosm experiment


ABSTRACT: 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

ORGANISM(S): marine metagenome

SUBMITTER: Jack Gilbert 

PROVIDER: E-GEOD-10119 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

altmetric image

Publications

Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.

Gilbert Jack A JA   Field Dawn D   Huang Ying Y   Edwards Rob R   Li Weizhong W   Gilna Paul P   Joint Ian I  

PloS one 20080822 8


<h4>Background</h4>Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities.<h4>Methodology/principal findings</h4>We p  ...[more]

Similar Datasets

2008-05-27 | E-GEOD-11074 | biostudies-arrayexpress
2008-07-06 | E-GEOD-11034 | biostudies-arrayexpress
2008-04-10 | E-GEOD-11019 | biostudies-arrayexpress
2014-12-22 | E-MTAB-2247 | biostudies-arrayexpress
2016-05-11 | GSE81262 | GEO
2011-03-17 | GSE27998 | GEO
2011-03-17 | E-GEOD-27998 | biostudies-arrayexpress
2021-03-13 | GSE168812 | GEO
| PRJEB12113 | ENA
2020-03-12 | PXD014327 | Pride