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| Status |
Public on Feb 08, 2008 |
| Title |
Metatranscriptomes of phytoplankton blooms from an ocean acidification mesocosm experiment |
| Organism |
marine metagenome |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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
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| Overall design |
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.
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| Contributor(s) |
Gilbert J, Field D, Li W, Edwards R, Joint I |
| Citation(s) |
18725995 |
| BioProject |
PRJNA28969 |
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| Submission date |
Jan 09, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Jack Anthony Gilbert |
| E-mail(s) |
jagi@pml.ac.uk
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| Phone |
01752 633 416
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| Fax |
01752 633 101
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| URL |
http://www.pml.ac.uk
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| Organization name |
Plymouth Marine Laboratory
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| Street address |
Prospect Place
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| City |
Plymouth |
| State/province |
Devon |
| ZIP/Postal code |
PL1 3DH |
| Country |
United Kingdom |
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| Platforms (1) |
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| Samples (4)
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| Relations |
| SRA |
SRP000101 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE10119_Biogeochemical_data.xls |
215.5 Kb |
(ftp)(http) |
XLS |
| GSE10119_Phytoplankton_identification.xls |
95.0 Kb |
(ftp)(http) |
XLS |
| Raw data are available in SRA |
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