Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016 (NCEI Accession 0291575)
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title: Microbial community composition from 16s V4 region amplicon sequencing of the methane Seep at the Cinder Cones Cold Seep site, Nov 2016 (NCEI Accession 0291575)
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abstract: This dataset contains data collected in the South Pacific Ocean and Southern Ocean from 2016-11-03 to 2016-11-15. These data include depth core. The instruments used to collect these data include Automated DNA Sequencer and PCR Thermal Cycler. These data were collected by Dr Andrew Thurber of Oregon State University as part of the "EAGER: Elucidating the Antarctic Methane Cycle at the Cinder Cones Reducing Habitat (Cinder Cone Seep)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2019-03-20. The following is the text of the dataset description provided by BCO-DMO: Microbial community composition of the Cinder Cones Cold Seep Dataset Description: This dataset includes details on 151 marine sediment community samples collected from the Cinder Cones Cold Seep site [-77.8, 166.666] in the Ross Sea region, Antarctica in November 2016. Data are uploaded to the NCBI Sequence Read Archive under submission SUB2655615 [ https://www.ncbi.nlm.nih.gov/bioproject/PRJNA387720 ] with a subset of the data from that archive originating from this project.
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supplementalInformation: Acquisition Description: Sediment cores were collected from the Cinder Cones site including a methane seep habitat and vertically sectioned into cm intervals with the exterior of the cores discarded to avoid vertical smearing. Sediments were placed in whirlpack bags and kept at -80 until DNA was extracted. Between 0.25 and 0.5 grams of frozen sediment had DNA extracted using the MoBio (now Qiagen) PowerSoil kits. Primers and amplification procedures follow the Earth Microbiome Project Protocol (http://www.earthmicrobiome.org/protocols-and-standards/16s/) using the updated primers in Apprill et al (2015) following Caporaso et al. (2011). In short, triplicate PCRs were run using the 515FB and the 806RB primers that copy the V4 region if the 16s rRNA gene. These primers were barcoded allowing later in silico separation of pooled samples. Controls and all samples were run on a gel to check for contamination. DNA was cleaned up using the MoBio UltraClean PCR Clean-Up Kit, samples were pooled into equal molar concentrations and submitted for sequencing. Data were de-multiplexed and primers trimmed. No other data manipulation has been performed.
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description: These data are available through the File Transfer Protocol (FTP). FTP is no longer supported by most internet browsers. You may copy and paste the FTP link to the data into an FTP client (e.g., FileZilla or WinSCP).
function: (CI_OnLineFunctionCode) download
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dataQualityInfo: (DQ_DataQuality)
scope: (DQ_Scope)
level: (MD_ScopeCode) dataset
lineage: (LI_Lineage)
processStep: (LE_ProcessStep)
description: NCEI Accession 0291575 v1.1 was published.
dateTime:
DateTime: 2024-04-21T18:25:23Z
output: (LE_Source)
sourceCitation: (CI_Citation)
title: NCEI Accession 0291575 v1.1
date: (CI_Date)
date: (inapplicable)
dateType: (CI_DateTypeCode) publication
citedResponsibleParty: (CI_ResponsibleParty)
individualName: (inapplicable)
contactInfo: (CI_Contact)
onlineResource: (CI_OnlineResource)
linkage: https://www.ncei.noaa.gov/archive/accession/0291575/1.1
protocol: HTTPS
name: NCEI Accession 0291575 v1.1
description: published 2024-04-21T18:25:23Z
function: (CI_OnLineFunctionCode) download
role: (inapplicable)
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metadataMaintenance: (MD_MaintenanceInformation)
maintenanceAndUpdateFrequency: (MD_MaintenanceFrequencyCode) asNeeded
maintenanceNote: Metadata are developed, maintained and distributed by NCEI. Updates are performed as needed to maintain currentness.
contact: (CI_ResponsibleParty)
organisationName: NOAA National Centers for Environmental Information
role: (CI_RoleCode) custodian
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acquisitionInformation: (MI_AcquisitionInformation)
instrument: (MI_Instrument)
identifier: (MD_Identifier)
code: PCR machine
type: PCR machine
description: thermal cycler, thermocycler, PCR machine, DNA amplifier The thermal cycler (also known as a thermocycler, PCR machine or DNA amplifier) is a laboratory apparatus most commonly used to amplify segments of DNA via the polymerase chain reaction (PCR). https://en.wikipedia.org/wiki/Thermal_cycler, 2017-05-02.
