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i_gilbert
s_BII-S-3
a_gilbert-assay-Gx
a_gilbert-assay-Tx
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| ONTOLOGY SOURCE REFERENCE | |||||||||
| Term Source Name | |||||||||
| Term Source File | |||||||||
| Term Source Version | |||||||||
| Term Source Description | |||||||||
| INVESTIGATION | |||||||||
| Investigation Identifier | 1.394538582604E12 | ||||||||
| Investigation Title | |||||||||
| Investigation Description | |||||||||
| Investigation Submission Date | |||||||||
| Investigation Public Release Date | |||||||||
| Comment [Created with configuration] | |||||||||
| Comment [Last Opened With Configuration] | |||||||||
| Comment[Created With Configuration] | |||||||||
| Comment[Last Opened With Configuration] | |||||||||
| INVESTIGATION PUBLICATIONS | |||||||||
| Investigation PubMed ID | |||||||||
| Investigation Publication DOI | |||||||||
| Investigation Publication Author List | |||||||||
| Investigation Publication Title | |||||||||
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| Investigation Publication Status Term Accession Number | |||||||||
| Investigation Publication Status Term Source REF | |||||||||
| INVESTIGATION CONTACTS | |||||||||
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| Investigation Person Roles Term Accession Number | |||||||||
| Investigation Person Roles Term Source REF | |||||||||
| STUDY | |||||||||
| Study Identifier | BII-S-3 | ||||||||
| Study Title | Metagenomes and Metatranscriptomes of phytoplankton blooms from an ocean acidification mesocosm experiment | ||||||||
| Study 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. 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. | ||||||||
| Comment[Study Grant Number] | |||||||||
| Comment[Study Funding Agency] | |||||||||
| Study Submission Date | 2008-08-15T0:0:0+0000 | ||||||||
| Study Public Release Date | 2008-08-15T0:0:0+0000 | ||||||||
| Study File Name | s_BII-S-3.txt | ||||||||
| STUDY DESIGN DESCRIPTORS | |||||||||
| Study Design Type | time series design | ||||||||
| Study Design Type Term Accession Number | |||||||||
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| STUDY PUBLICATIONS | |||||||||
| Study PubMed ID | 18725995 | 18783384 | |||||||
| Study Publication DOI | 10.1371/journal.pone.0003042 | 10.1111/j.1462-2920.2008.01745.x | |||||||
| Study Publication Author List | Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. | Gilbert JA, Thomas S, Cooley NA, Kulakova A, Field D, Booth T, McGrath JW, Quinn JP, Joint I. | |||||||
| Study Publication Title | Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. | Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters. | |||||||
| Study Publication Status | indexed in PubMed | indexed in PubMed | |||||||
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| STUDY FACTORS | |||||||||
| Study Factor Name | dose | compound | collection time | ||||||
| Study Factor Type | dose | chemical compound | time | ||||||
| Study Factor Type Term Accession Number | |||||||||
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| STUDY ASSAYS | |||||||||
| Study Assay File Name | a_gilbert-assay-Gx.txt | a_gilbert-assay-Tx.txt | |||||||
| Study Assay Measurement Type | metagenome sequencing | transcription profiling | |||||||
| Study Assay Measurement Type Term Accession Number | 0000424 | ||||||||
| Study Assay Measurement Type Term Source REF | OBI | OBI | |||||||
| Study Assay Technology Type | nucleotide sequencing | nucleotide sequencing | |||||||
| Study Assay Technology Type Term Accession Number | |||||||||
| Study Assay Technology Type Term Source REF | OBI | OBI | |||||||
| Study Assay Technology Platform | 454 Genome Sequencer FLX | 454 Genome Sequencer FS | |||||||
| STUDY PROTOCOLS | |||||||||
| Study Protocol Name | sample collection - standard procedure 1 | nucleic acid extraction - standard procedure 2 | mRNA extraction - standard procedure 3 | genomic DNA extraction - standard procedure 4 | reverse transcription - standard procedure 5 | pyrosequencing - standard procedure 6 | sequence analysis - standard procedure 7 | ||
| Study Protocol Type | environmental material collection | nucleic acid extraction | RNA extraction | DNA extraction | reverse transcription | DNA sequencing | DNA sequencing | ||
| Study Protocol Type Term Accession Number | |||||||||
| Study Protocol Type Term Source REF | |||||||||
| Study Protocol Description | Waters samples were prefiltered through a 1.6 um GF/A glass fibre filter to reduce Eukaryotic contamination. Filtrate was then collected on a 0.2 um Sterivex (millipore) filter which was frozen in liquid nitrogen until nucelic acid extraction. CO2 bubbled through 11000 L mesocosm to simulate ocean acidification predicted conditions. Then phosphate and nitrate were added to induce a phytoplankton bloom. | Total nucleic acid extraction was done as quickly as possible using the method of Neufeld et al, 2007. | RNA MinElute + substrative Hybridization + MEGAclear For transcriptomics, total RNA was separated from the columns using the RNA MinElute clean-up kit (Qiagen) and checked for integrity of rRNA using an Agilent bioanalyser (RNA nano6000 chip). High integrity rRNA is essential for subtractive hybridization. Samples were treated with Turbo DNA-free enzyme (Ambion) to remove contaminating DNA. The rRNA was removed from mRNA by subtractive hybridization (Microbe Express Kit, Ambion), and absence of rRNA and DNA contamination was confirmed using the Agilent bioanalyser. The mRNA was further purified with the MEGAclearTM kit (Ambion). Reverse transcription of mRNA was performed using the SuperScript III enzyme (Invitrogen) with random hexamer primers (Promega). The cDNA was treated with RiboShredderTM RNase Blend (Epicentre) to remove trace RNA contaminants. To improve the yield of cDNA, samples were subjected to random amplification using the GenomiPhi V2 method (GE Healthcare). GenomiPhi technology produces branched DNA molecules that are recalcitrant to the pyrosequencing methodology. Therefore amplified samples were treated with S1 nuclease using the method of Zhang et al.2006. | superscript+random hexamer primer | 1. Sample Input and Fragmentation: The Genome Sequencer FLX System supports the sequencing of samples from a wide variety of starting materials including genomic DNA, PCR products, BACs, and cDNA. Samples such as genomic DNA and BACs are fractionated into small, 300- to 800-base pair fragments. For smaller samples, such as small non-coding RNA or PCR amplicons, fragmentation is not required. Instead, short PCR products amplified using Genome Sequencer fusion primers can be used for immobilization onto DNA capture beads as shown below. | ||||
| Study Protocol URI | |||||||||
| Study Protocol Version | |||||||||
| Study Protocol Parameters Name | filter pore size | ||||||||
| Study Protocol Parameters Name Term Accession Number | |||||||||
| Study Protocol Parameters Name Term Source REF | |||||||||
| Study Protocol Components Name | 454 GS-FLX | ||||||||
| Study Protocol Components Type | DNA sequencer | ||||||||
| Study Protocol Components Type Term Accession Number | |||||||||
| Study Protocol Components Type Term Source REF | |||||||||
| STUDY CONTACTS | |||||||||
| Study Person Last Name | Gilbert | Field | Huang | Edwards | Li | Gilna | Joint | ||
| Study Person First Name | Jack | Dawn | Ying | Rob | Weizhong | Paul | Ian | ||
| Study Person Mid Initials | A | ||||||||
| Study Person Email | jagi@pml.ac.uk | ||||||||
| Study Person Phone | |||||||||
| Study Person Fax | |||||||||
| Study Person Address | Prospect Place, Plymouth, United Kingdom | CEH Oxford, Oxford, United Kingdom | San Diego State University, San Diego, California, United States of America | Argonne National Laboratory, Argonne, Illinois, United States of America | San Diego State University, San Diego, California, United States of America | San Diego State University, San Diego, California, United States of America | Prospect Place, Plymouth, United Kingdom | ||
| Study Person Affiliation | Plymouth Marine Laboratory | NERC Centre for Ecology and Hydrology | California Institute for Telecommunications and Information Technology | Department of Computer Science, Mathematics and Computer Science Division, | California Institute for Telecommunications and Information Technology | California Institute for Telecommunications and Information Technology | Plymouth Marine Laboratory | ||
| Study Person Roles | principal investigator role | principal investigator role | principal investigator role | principal investigator role | principal investigator role | principal investigator role | principal investigator role | ||
| Study Person Roles Term Accession Number | |||||||||
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| Comment[Study Person REF] | |||||||||
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| Source Name | Characteristics[organism] | Term Source REF | Term Accession Number | Characteristics[geographical location] | Term Source REF | Term Accession Number | Characteristics[latitude] | Term Source REF | Term Accession Number | Characteristics[longitude] | Term Source REF | Term Accession Number | Characteristics[chlorophyll a concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[fucoxanthin concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[peridinin concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[butfucoxanthin concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[hexfucoxanthin concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[alloxanthin concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[zeaxanthin concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[lutein concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[chl-c3 concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[chl-c2 concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[prasinoxanthin concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[neoxanthin concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[violaxanthin concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[diadinoxanthin concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[diatoxanthin concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[divinyl-chl-b concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[chl-b concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[divinyl-chl-a concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[chl-a concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[BB carotene concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[bacteria count] | Unit | Term Source REF | Term Accession Number | Characteristics[synechococcus count] | Unit | Term Source REF | Term Accession Number | Characteristics[small picoeukaryotes count] | Unit | Term Source REF | Term Accession Number | Characteristics[large picoeukaryotes count] | Unit | Term Source REF | Term Accession Number | Characteristics[nanoflagellates count] | Unit | Term Source REF | Term Accession Number | Characteristics[cryptophytes count] | Unit | Term Source REF | Term Accession Number | Characteristics[phosphate concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[nitrate concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[particulate organic nitrogen concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[particulate organic carbon concentration] | Unit | Term Source REF | Term Accession Number | Characteristics[primary production depth integrated production to 3 m expressed_in mgC m-2 d-1] | Unit | Term Source REF | Term Accession Number | Characteristics[water salinity] | Unit | Term Source REF | Term Accession Number | Characteristics[fluorescence] | Term Source REF | Term Accession Number | Characteristics[water temperature at 3 meter depth] | Unit | Term Source REF | Term Accession Number | Protocol REF | Parameter Value[filter pore size] | Unit | Term Source REF | Term Accession Number | Sample Name | Factor Value[compound] | Term Source REF | Term Accession Number | Factor Value[dose] | Term Source REF | Term Accession Number | Factor Value[collection time] | Term Source REF | Term Accession Number |
| GSM255770 | marine metagenome | Norway, fjord, coastal | 5 13' 20'' E | 60 16' 10'' N | 9.23 | ug/l | 0.54 | ug/l | 0.18 | ug/l | 0.14 | ug/l | 0.82 | ug/l | 0.36 | ug/l | 0.35 | ug/l | 0.37 | ug/l | 0.29 | ug/l | 0.59 | ug/l | 0 | ug/l | 0 | ug/l | 0.64 | ug/l | 0.46 | ug/l | 0.1 | ug/l | 0 | ug/l | 5.25 | ug/l | 0 | ug/l | 9.23 | ug/l | 0.72 | ug/l | 4666004 | number/ml | 7064 | number/ml | 36257 | number/ml | 5450 | number/ml | 2851 | number/ml | 660 | number/ml | 0.23 | umol/l | 7.53 | umol/l | 143 | ug/l | 844 | ug/l | 591.4 | mg/m2/d | 31.3 | psu | 17.6 | 9.7 | degree celsius | sample collection - standard procedure 1 | 0.22 | micrometer | GSM255770 | CO2 | high | may 13th, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| GSM255771 | marine metagenome | Norway, fjord, coastal | 5 13' 20'' E | 60 16' 10'' N | 11.22 | ug/l | 1.43 | ug/l | 0.14 | ug/l | 0.17 | ug/l | 1.15 | ug/l | 0.33 | ug/l | 0.23 | ug/l | 0.41 | ug/l | 0.65 | ug/l | 0.87 | ug/l | 0 | ug/l | 0 | ug/l | 0.99 | ug/l | 0.64 | ug/l | 0.11 | ug/l | 0 | ug/l | 5.97 | ug/l | 0 | ug/l | 11.22 | ug/l | 0.83 | ug/l | 4862861 | number/ml | 13867 | number/ml | 38513 | number/ml | 12035 | number/ml | 4390 | number/ml | 1702 | number/ml | 0.19 | umol/l | 3.84 | umol/l | 104 | ug/l | 561 | ug/l | 938.1 | mg/m2/d | 31.4 | psu | 23.6 | 9.6 | degree celsius | sample collection - standard procedure 1 | 0.22 | micrometer | GSM255771 | CO2 | normal | may 13th, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| GSM255772 | marine metagenome | Norway, fjord, coastal | 5 13' 20'' E | 60 16' 10'' N | 1.6 | ug/l | 0.21 | ug/l | 0.41 | ug/l | 0.06 | ug/l | 0.15 | ug/l | 0.03 | ug/l | 0.13 | ug/l | 0.02 | ug/l | 0.05 | ug/l | 0.31 | ug/l | 0 | ug/l | 0 | ug/l | 0.05 | ug/l | 0.2 | ug/l | 0.04 | ug/l | 0 | ug/l | 0.21 | ug/l | 0 | ug/l | 1.6 | ug/l | 0.06 | ug/l | 9516120 | number/ml | 16465 | number/ml | 21435 | number/ml | 878 | number/ml | 138 | number/ml | 75 | number/ml | 0.2 | umol/l | 3.94 | umol/l | 128 | ug/l | 783 | ug/l | 118 | mg/m2/d | 31.5 | psu | 4.5 | 9 | degree celsius | sample collection - standard procedure 1 | 0.22 | micrometer | GSM255772 | CO2 | high | may 19th, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| GSM255773 | marine metagenome | Norway, fjord, coastal | 5 13' 20'' E | 60 16' 10'' N | 1.77 | ug/l | 0.19 | ug/l | 0.26 | ug/l | 0.03 | ug/l | 0.27 | ug/l | 0.05 | ug/l | 0.13 | ug/l | 0.02 | ug/l | 0.07 | ug/l | 0.3 | ug/l | 0 | ug/l | 0 | ug/l | 0.1 | ug/l | 0.21 | ug/l | 0.05 | ug/l | 0 | ug/l | 0.43 | ug/l | 0 | ug/l | 1.77 | ug/l | 0.12 | ug/l | 6143892 | number/ml | 22049 | number/ml | 42927 | number/ml | 2916 | number/ml | 283 | number/ml | 216 | number/ml | 0.25 | umol/l | 0.59 | umol/l | 166 | ug/l | 945 | ug/l | 129.9 | mg/m2/d | 31.5 | psu | 4.1 | 8.9 | degree celsius | sample collection - standard procedure 1 | 0.22 | micrometer | GSM255773 | CO2 | normal | may 19th, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Sample Name | Protocol REF | Protocol REF | Extract Name | Material Type | Term Source REF | Term Accession Number | Protocol REF | Assay Name | Protocol REF | Protocol REF | Raw Data File |
| GSM255770 | nucleic acid extraction - standard procedure 2 | mRNA extraction - standard procedure 3 | GSM255770.e1 | mRNA | reverse transcription - standard procedure 5 | assay1 | pyrosequencing - standard procedure 6 | sequence analysis - standard procedure 7 | ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000266/EWOEPZA01.sff | ||
| GSM255771 | nucleic acid extraction - standard procedure 2 | mRNA extraction - standard procedure 3 | GSM255771.e1 | mRNA | reverse transcription - standard procedure 5 | assay2 | pyrosequencing - standard procedure 6 | sequence analysis - standard procedure 7 | ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000266/EWOEPZA02.sff | ||
| GSM255772 | nucleic acid extraction - standard procedure 2 | mRNA extraction - standard procedure 3 | GSM255772.e1 | mRNA | reverse transcription - standard procedure 5 | assay3 | pyrosequencing - standard procedure 6 | sequence analysis - standard procedure 7 | ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000266/EXHS9OF01.sff | ||
| GSM255772 | nucleic acid extraction - standard procedure 2 | mRNA extraction - standard procedure 3 | GSM255772.e1 | mRNA | reverse transcription - standard procedure 5 | assay3 | pyrosequencing - standard procedure 6 | sequence analysis - standard procedure 7 | ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000266/EX398L102.sff | ||
| GSM255773 | nucleic acid extraction - standard procedure 2 | mRNA extraction - standard procedure 3 | GSM255773.e1 | mRNA | reverse transcription - standard procedure 5 | assay4 | pyrosequencing - standard procedure 6 | sequence analysis - standard procedure 7 | ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000266/EXHS9OF02.sff | ||
| GSM255773 | nucleic acid extraction - standard procedure 2 | mRNA extraction - standard procedure 3 | GSM255773.e1 | mRNA | reverse transcription - standard procedure 5 | assay4 | pyrosequencing - standard procedure 6 | sequence analysis - standard procedure 7 | ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000266/EX398L101.sff | ||
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