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SRX2058520: Metagenomic sequencing Soudan Mine gDNA
1 ILLUMINA (Illumina HiSeq 1000) run: 16M spots, 1.8G bases, 646.6Mb downloads

Design: Metagenomic shotgun sequencing (Hiseq): We use Picogreen (Invitrogen) to quantitate genomic DNA samples. DNA is sheared using a Covaris and libraries were constructed with the Nugen Ovation Ultralow Library protocol. We aim for an insert size of 175bp to enable read merging. Amplified libraries are visualized on an Agilent DNA1000 chip or Caliper HiSens Bioanalyzer assay, pooled at equimolar concentrations based on these results, and size selected using a Sage PippinPrep 2% cassette. The library pool is quantified using a Kapa Biosystems qPCR library quantification kit, then sequenced on the Illumina HiSeq1000 in a 2x100 paired-end sequencing run using dedicated read indexing. The samples are demultiplexed with CASAVA 1.8.2.
Submitted by: Marine Biological Laboratory
Study: Soudan Iron Mine Metagenome
show Abstracthide Abstract
Embedded deep within northern Minnesota's expansive Iron Range, the Soudan Iron Mine (47°49'24? N, 92°14'14? W) transects massive veins of hematite and Archaean (2.7 Gy) banded iron formations, reaching a depth of 713 m (2,341 ft) below the surface. Now an actively maintained State Park serving to preserve Minnesota's oldest and deepest underground mine, Soudan provides year-round access to the deep terrestrial subsurface and the unique microbial communities it hosts. Before mining ceased in 1962, vertical and horizontal exploratory cores were taken at its lowest level (Level 27, 713 m depth) to track the iron formation. Today these boreholes act as conduits for anoxic, low flow, saline groundwater in an otherwise dry mine. Calcium chloride brines emanate from seeps with ionic strengths up to three times saltier than seawater, low oxidation-reduction potentials, circumneutral pH, and low concentrations of organic electron donors. Despite carbon limitation, anoxic brines contain reduced metals and continuously evolve methane gas, raising questions about the microbes responsible for primary production and carbon flux in this subsurface ecosystem.
Sample:
SAMN05712325 • SRS1650503 • All experiments • All runs
Library:
Name: DDH951
Instrument: Illumina HiSeq 1000
Strategy: WGS
Source: METAGENOMIC
Selection: RANDOM
Layout: PAIRED
Runs: 1 run, 16M spots, 1.8G bases, 646.6Mb
Run# of Spots# of BasesSizePublished
SRR407225616,000,0001.8G646.6Mb2016-08-30

ID:
3052706

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