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Metagenome-assembled genome: SRR12480113_metabat2_3

Identifiers
BioSample: SAMEA115425311; SRA: ERS18571007
Organism
Fragilariopsis cylindrus CCMP1102
cellular organisms; Eukaryota; Sar; Stramenopiles; Ochrophyta; Bacillariophyta; Bacillariophyceae; Bacillariophycidae; Bacillariales; Bacillariaceae; Fragilariopsis; Fragilariopsis cylindrus
Attributes
broad-scale environmental contextwater
collection date2017-01-28T04:45:00Z
environmental mediumgo-ship
geographic locationSouthern Ocean
investigation typemetagenome-assembled genome
isolation sourcemarine metagenome
project nameThe Global Ocean Shipboard Hydrographic Investigations Program (GO-SHIP) is a ship-based global survey of ocean hydrographic sections, which are repeatedly measured on a decadal time scale. The program covers a suite of physical (light, heat, currents, water column structure, etc.) and chemical (nutrients, oxygen, dissolved organic and inorganic carbon, pH, etc.) state variables over the full ocean water column, and in areas of the ocean inaccessible to other platforms. The principal scientific objectives for GO-SHIP are: (1) understanding and documenting the large-scale ocean water property distributions, their changes, and drivers of those changes, and (2) addressing questions of how a future ocean will increase in dissolved inorganic carbon, become more acidified and more stratified, and experience changes in circulation and ventilation processes due to global warming and altered water cycle.</p><p>The vision of the biological GO-SHIP initiative, or "Bio-GO-SHIP," is to develop a deep understanding of the link between the physio-chemical environment and global ocean plankton diversity, abundance, and biogeochemical roles in the context of a changing ocean. This will be achieved through systematic, high-quality, and calibrated sampling of marine 'omics products.</p><p>In this BioProject, we aim to provide a singular resource for Bio-GO-SHIP 'omics datasets. We also provide appropriate metadata such that the 'omics data may be linked to the broad range of state variables measured by GO-SHIP and associated oceanographic transects.
sample nameSRR12480113_metabat2_3
ENA first public2024-03-20
ENA-CHECKLISTERC000047
INSDC center nameEMG
INSDC statuspublic
Submitter IdSRR12480113_metabat2_3
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaSPAdes_v3.15.2
binning parametersdefault
binning softwareMGnify-genomes-generation-pipeline_v1.0.0
broker nameEBI-EMG
completeness score73.5
completeness softwareEukCC_v2.1.0
contamination score0.28
geographic location (latitude)-70.00029300
geographic location (longitude)-100.24112000
local environmental contextocean
metagenomic sourcemarine metagenome
sample derived fromSAMN15783169
scientific_nameFragilariopsis cylindrus CCMP1102
sequencing methodIllumina NovaSeq 6000
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic run SRR12480113 of study SRP278138.

BioProject
PRJEB50181
Retrieve all samples from this project

Submission
EBI; 2024-06-04
Accession:
SAMEA115425311
ID:
41667582

BioProject Nucleotide

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  • Metagenome-assembled genome: SRR12480113_metabat2_3
    Metagenome-assembled genome: SRR12480113_metabat2_3
    biosample
  • Giraffa tRNA-Phe, 12S ribosomal RNA, tRNA-Val, 16S ribosomal RNA, and tRNA-Leu g...
    Giraffa tRNA-Phe, 12S ribosomal RNA, tRNA-Val, 16S ribosomal RNA, and tRNA-Leu genes, complete sequence; NADH dehydrogenase subunit 1 (ND1) gene, complete cds; tRNA-Ile, tRNA-Gln, and tRNA-Met genes, complete sequence; NADH dehydrogenase subunit 2 (ND2) gene, complete cds; tRNA-Trp, tRNA-Ala, tRNA-Asn, tRNA-Cys, and tRNA-Tyr genes, complete sequence; cytochrome c oxidase subunit I (COX1) gene, complete cds; tRNA-Ser and tRNA-Asp genes, complete sequence; cytochrome c oxidase subunit II (COX2) gene, complete cds; tRNA-Lys gene, complete sequence; ATP synthase F0 subunit 8 (ATP8), ATP synthase F0 subunit 6 (ATP6), and cytochrome c oxidase subunit III (COX3) genes, complete cds; tRNA-Gly gene, complete sequence; NADH dehydrogenase subunit 3 (ND3) gene, complete cds; tRNA-Arg gene, complete sequence; NADH dehydrogenase subunit 4L (ND4L) and NADH dehydrogenase subunit 4 (ND4) genes, complete cds; tRNA-His, tRNA-Ser, and tRNA-Leu genes, complete sequence; NADH dehydrogenase subunit 5 (ND5) and NADH dehydrogenase subunit 6 (ND6) genes, complete cds; tRNA-Glu gene, complete sequence; cytochrome b (CYTB) gene, complete cds; and tRNA-Thr and tRNA-Pro genes and control region, complete sequence; mitochondrial.
    PopSet: 2032036563
    PopSet
  • PREDICTED: Chaetura pelagica CDC42 binding protein kinase beta (DMPK-like) (CDC4...
    PREDICTED: Chaetura pelagica CDC42 binding protein kinase beta (DMPK-like) (CDC42BPB), mRNA
    gi|701408867|ref|XM_009999807.1|
    Nucleotide
  • Microgastrinae sp. WMIC0122 cytochrome oxidase subunit 1 (COI) gene, partial cds...
    Microgastrinae sp. WMIC0122 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial
    gi|331262881|gnl|uoguelph|ASCNC312- I-5P|gb|JF863239.1|
    Nucleotide
  • Beta-galactosidase [Caenorhabditis elegans]
    Beta-galactosidase [Caenorhabditis elegans]
    gi|72000600|ref|NP_505849.2|
    Protein

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