characteristics.text: SAMN39735874
characteristics.characteristic: External Id
characteristics.text: Oregon State University
characteristics.characteristic: INSDC center name
characteristics.text: 2025-02-01T00:52:18.223Z
characteristics.characteristic: INSDC first public
characteristics.text: 2025-02-01T00:52:18.223Z
characteristics.characteristic: INSDC last update
characteristics.text: SRS20355613
characteristics.characteristic: INSDC secondary accession
characteristics.text: live
characteristics.characteristic: INSDC status
characteristics.text: MIMS.me
characteristics.characteristic: NCBI submission model
characteristics.text: MIGS/MIMS/MIMARKS.water
characteristics.characteristic: NCBI submission model
characteristics.text: MIMS.me.water.6.0
characteristics.characteristic: NCBI submission package
characteristics.text: SRS20355613
characteristics.characteristic: SRA accession
characteristics.text: 2021-07-30
characteristics.characteristic: collection_date
characteristics.text: Collected by lowering tubing to desired depth and filling sample bottles using a peristalitic pump
characteristics.characteristic: collection_method
characteristics.text: 0.02
characteristics.characteristic: depth
characteristics.text: Metatranscriptome with added internal control sequences and reduced rRNA sequences
characteristics.characteristic: description
characteristics.text: polar [ENVO:01000339]
characteristics.characteristic: env_broad_scale
characteristics.text: estuary [ENVO:00000045]
characteristics.characteristic: env_local_scale
characteristics.text: estuarine water [ENVO:01000301]
characteristics.characteristic: env_medium
characteristics.text: USA: Elson Lagoon, Alaska
characteristics.characteristic: geo_loc_name
characteristics.text: 71.328940 N 156.564790 W
characteristics.characteristic: lat_lon
characteristics.text: marine metagenome
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_408172
characteristics.characteristic: organism
characteristics.text: 7.93
characteristics.characteristic: ph
characteristics.text: a
characteristics.characteristic: replicate
characteristics.text: 19.12
characteristics.characteristic: salinity
characteristics.text: Sample collected on a 0.2 micron pore-size Sterivex-GP filter (MilliporeSigma), preserved with RNAlater buffer (Qiagen), and stored frozen at -80C until processed
characteristics.characteristic: samp_collect_device
characteristics.text: Internal control RNA fragments (4-20 ng) produced with DNA fragments (s6, s8, and s15) that were PCR amplified from Saccharolobus solfataricus strain DMS 1617 (ATCC 35092, Manassas, VA) were added to samples prior to extraction as described in Gifford et al. (2016, DOI 10.1128/mBio.01279-16). RNA and DNA were co-extracted from 0.22 µm Sterivex filters using ZymoBIOMICS DNA/RNA Miniprep Kits (Zymo Research, Irvine, CA), and RNA was purified and treated with DNase to remove DNA using the RNA Clean & Concentrator-5 kit (Zymo Research, Irvine, CA). Metatranscriptomic libraries were generated using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina, San Diego, CA) according to manufacturer instructions. Libraries were sequenced at the University of Oregon Genomics & Cell Characterization Core Facility on the Illumina Novaseq 6000 platform using an S4 300 cycle 2x150bp paired-end run configuration.
characteristics.characteristic: samp_mat_process
characteristics.text: 7.1
characteristics.characteristic: temp
characteristics.text: Shotgun metatranscriptome sequences of water column microbial community: estuary sample BLERM2021-015a-w
characteristics.characteristic: title
characteristics.text: 0.6
characteristics.characteristic: tot_depth_water_col