<div><p>Water column samples were collected with a 12 L Niskin bottles housed on a rosette (General Oceanics) equipped with a SBE- 911plus conductivity-temperature-depth (CTD) sensor (Sea- Bird Electronics). Determination of oxygen concentration at selected depths was carried out using the Winkler method with an automatic endpoint detection burette (716 DNS Titrino, Metrohm AG). Water from two distinct horizons (each representing a distinct range of salinity and oxygen between the top and bottom of each Niskin bottle) was collected from the Thetis interface; the upper interface (UI) layer corresponding to 7.0 – 16.3% salinity, and the lower (LI) layer with 21.4 – 27.6% salinity. Oxygen in the UI sample ranged from 9.5 μmol L-1 to undetectable, and remained undetectable in the lower sample. From each horizon, ca. 12 L of water were collected on Durapore membranes (47 mm, 0.65 μm, Millipore) under gentle pressure (~100 ml min−1), using a peristaltic pump (Ecoline ISM 1079). The filters were stored in RNA Shield at -80oC until analysis. The filters were transferred into Lysing Matrix E tubes (MP Biomedicals). Four ml of RNeasy Midi Kit Buffer RTL (Qiagen) were added, homogenized for 60 seconds at 4.0 m/s using a FastPrep®-24 (MP Biomedicals), and centrifuged for 10 minutes at 4,000 x g. Liquids were transferred to clean tubes, 1 volume of 70% ethanol was added to each tube, and extracts were processed following the RNeasy kit instructions. Extractions were treated with DNase and purified with the MEGA Clear kit as described above. Fluid and filter extracts were combined for each sample and concentrated by ethanol precipitation. Absence of DNA was confirmed by 40 cycles of PCR using the general bacterial SSU rRNA gene primer 8F and the universal primer 1492R. For each extraction of total RNA (two replicates per depth horizon), cDNA was synthesized using the Ovation RNA-Seq System V2 Kit (NuGEN) following the manufacturer's instructions. Finally, cDNAs were purified with the MinElute Reaction Cleanup Kit (Qiagen) and sent for paired-end sequencing. One lane of Illumina HiSeq 2x100bp was requested for each sample (two replicates per lane). </p></div>
Microbial metatranscriptomics: upper and lower halocline water column
<div><p>Metatranscriptome of whole microbial community from upper and lower halocline water column of Thetis DHAB</p>
<p><strong>Related Reference:</strong></p>
<p>Pachiadaki, M.G., Yakimov, M.M., Leadbetter, E., Edgcomb, V.P. 2014. Unveiling microbial activities along the halocline of Thetis, a deep hypersaline anoxic basin in the Eastern Mediterranean Sea. The ISME J. doi:10.1038/ismej.2014.100.</p></div>
metatranscriptomics - upper_lower halocline
<div><p>Forward and reverse reads were paired and filtered for quality control using CLC Genomics Workbench 5.0 (CLCBio) and a minimum quality score of 28, a minimum read length of 94 bp, allowing no sequences with ambigious nucleotides. The same platform was used to perform assembly of contigs and mapping of reads to contigs. The Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline was used through the CAMERA platform to assign contigs to clusters of orthologous gene (COG) families, gene ontologies (GO), and protein families (Pfam) using four translation tables.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- original file: EdgcombThetisMetatranscriptomeData_final.xlsx<br />
- added conventional header with dataset name, PI name, version date<br />
- renamed parameters to BCO-DMO standard<br />
- added cruise id, lat, lon<br />
- added html links to GenBank BioProject</p>
<p> </p></div>
554030
metatranscriptomics - upper_lower halocline
2015-03-24T14:42:39-04:00
2015-03-24T14:42:39-04:00
2023-07-07T16:10:26-04:00
urn:bcodmo:dataset:554030
Microbial metatranscriptomics: upper and lower halocline water column data from the R/V Urania cruise in the Mediterranean Sea during 2012 (Pickled Protists project)
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Edgcomb, V. P., Bernhard, J. M. (2015) Microbial metatranscriptomics: upper and lower halocline water column data from the R/V Urania cruise in the Mediterranean Sea during 2012 (Pickled Protists project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-03-19) Version Date 2015-03-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/554030 [access date]
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