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Sampling of cores was done in accordance with IODP protocols.<\/p>\n
All C0014 samples were cored on 16 September 2010 via via HPCS (hydraulic piston coring system).
\nAll C0015 samples were cored on 18 September 2010 via HPCS.
\nAll C0017 samples were cored on 27 September 2010 via HPCS.<\/p>\n
Core sections were kept frozen (-80\u00b0C) until DNA extractions. RNA was extracted using a phenol chloroform protocol. The RNA extract was DNAse treated using the Invitrogen\u2122 Ambion\u2122 Turbo DNA-free Kit and purified using the Qiagen\u00ae RNeasy Mini Kit. A cDNA library was made using the Qiagen \u00ae QuantiTec Reverse Transcription Kit. Polymerase chain reactions used the KAPABiosystems\u00ae KAPA2G Robust HotStart ReadyMix PCR Kit for 32 cycles.<\/p>\n
Sequencing of the product was performed on the Illumina\u00ae MiSeq 2500.<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/ocean-data.org\/schema\/hasBriefDescription":[{"@value":"16S rRNA gene (from RNA)","@language":"en-US"}],"http:\/\/purl.org\/dc\/terms\/description":[{"@value":"
Next-generation sequencing data across a hydrothermal gradient; Okinawa Backarc Basin IODP 331 \u2013 subvent biosphere.\u00a0RNA extractions were attempted from sediments at Sites C0014 and C0017 to selectively investigate the active microbial populations at these sites. This study was conducted to supplement the gene-based and metagenomic studies. However, the results from sequenced reverse transcribe 16S rRNA demonstrate the sensitivity of extraction and amplification to external nucleic acids and attest to the challenges in working with low biomass environmental samples. Inconsistencies between primersets and replicates make conclusions about the results of this RNA study extremely tenuous.<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/www.w3.org\/2000\/01\/rdf-schema#label":[{"@value":"16S rRNA gene from RNA","@type":"xsd:string"}],"http:\/\/ocean-data.org\/schema\/hasProcessingDescription":[{"@value":"
Data Processing: Demultiplexing was performed in Mothur (v.1.30.1).<\/p>\n
Problem report:\u00a0<\/strong>Upon analysis, the RNA dataset does not appear to reflect the same or similar information as the published 16S rRNA gene amplicon dataset. Rather, it indicates significant background noise from extraction and not an indigenous representation of the subsurface biosphere.<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/purl.org\/dc\/terms\/identifier":[{"@value":"781114","@type":"xsd:int"}],"http:\/\/purl.org\/dc\/terms\/title":[{"@value":"16S rRNA gene from RNA"}],"http:\/\/purl.org\/dc\/terms\/date":[{"@value":"2019-11-06T16:03:22-05:00","@type":"xsd:dateTime"}],"http:\/\/purl.org\/dc\/terms\/created":[{"@value":"2019-11-06T16:03:22-05:00","@type":"xsd:dateTime"}],"http:\/\/purl.org\/dc\/terms\/modified":[{"@value":"2023-07-07T16:10:26-04:00","@type":"xsd:dateTime"}],"http:\/\/rdfs.org\/ns\/void#inDataset":[{"@id":"http:\/\/www.bco-dmo.org\/"}],"http:\/\/ocean-data.org\/schema\/namedGraph":[{"@value":"urn:bcodmo:dataset:781114","@type":"xsd:token"}],"http:\/\/ocean-data.org\/schema\/osprey_page":[{"@id":"https:\/\/www.bco-dmo.org\/dataset\/781114"}],"http:\/\/ocean-data.org\/schema\/identifier":[{"@value":"_:Identifier781114"}],"http:\/\/ocean-data.org\/schema\/datasetTitle":[{"@value":"16S rRNA gene (from RNA) from samples collected on cruise Chikyu-331 in the Okinawa Trough, Japan from September to October 2010","@language":"en-US"}],"http:\/\/ocean-data.org\/schema\/abstract":[{"@value":"RNA extractions were attempted from sediments at Sites C0014 and C0017 to selectively investigate the active microbial populations at these sites. 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