No analyses found in MGnify
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Access samples and data collected and generated by the HoloFood project.
Sample data for SAMEA8141778, a HoloFood metatranscriptomic salmon sample
Metadata for sample SAMEA8141778, stored in BioSamples and ENA.
Download all as TSV| Marker | Measurement | Units |
|---|---|---|
| ENA-CHECKLIST | ERC000052 | None |
| ENA-FIRST-PUBLIC | 2023-03-22 | None |
| ENA-LAST-UPDATE | 2023-03-22 | None |
| External Id | SAMEA8141778 | None |
| INSDC center alias | UNIVERSITY OF COPENHAGEN | None |
| INSDC center name | UNIVERSITY OF COPENHAGEN | None |
| INSDC first public | 2023-03-22T12:21:32Z | None |
| INSDC last update | 2023-03-22T12:21:32Z | None |
| INSDC status | public | None |
| SRA accession | ERS5828591 | None |
| Submitter Id | SB04_05C1a_metaT | None |
| adapters | AGATCGGAAGAGCACACGTCTGAACTCCAGTCA;AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT | None |
| collection date | 2019-08-14 | None |
| description | Salmon meta transcriptomic data from Distal gut content; animal SB04.05 from tank SB04 with treatment Saturn | None |
| geographic location (country and/or sea) | Norway | None |
| geographic location (latitude) | 66.08 | DD |
| geographic location (longitude) | 12.588 | DD |
| geographic location (region and locality) | Dønna; Nordland county | None |
| host body site | Distal gut content | None |
| host common name | Atlantic salmon | None |
| host diet | Sanford Blue Mussel Meal | None |
| host diet treatment | Saturn: SB 4.4% blue mussel meal | None |
| host diet treatment concentration | 0 | % mass |
| host disease status | Wounded:- | None |
| host gutted mass | 160.2 | g |
| host length | 26 | cm |
| host scientific name | Salmo salar | None |
| host storage container | LetSea Tank: Saturn | None |
| host storage container pH | 7.05 | None |
| host storage container temperature | 12.76 | °C |
| host subject id | SB04.05 | None |
| host taxid | 8030 | None |
| host total mass | 186.8 | g |
| library name | Illumina Ribo-Zero Plus rRNA Depletion Kit + NEB Next Ultra RNA Library Prep Kit | None |
| library selection | rRNA depletion + strand specific library | None |
| nucleic acid extraction | D-rex protocol | None |
| organism | fish gut metagenome | None |
| project | HoloFood | None |
| project name | HoloFood Salmon - MetaTranscriptomics | None |
| reference host genome for decontamination | GCA_000000000.0 | None |
| sample storage buffer | Shield | None |
| sample storage container | 2ml E-matrix | None |
| sample storage location | UCPH | None |
| sample storage temperature | -20 | °C |
| sample volume or weight for DNA extraction | 0.2 | mL |
| scientific_name | fish gut metagenome | None |
| sequencing method | Illumina NovaSeq 6000 | None |
| title | SB04.05C1a | None |
| trial timepoint | 0 | day |
| Marker | Measurement | Units |
|---|---|---|
| Body site | distal gut content | None |
| Experiment | metatranscriptomics | None |
| Index PCR cycles | 12 | None |
| Lab Process ID | LPS00755 | None |
| Omics | Metagenomics | None |
| Organism | Salmon | None |
| Pool | S-MG-P13-514 | None |
| Project | HoloFood | None |
| Raw seq. name | S-MG-P13-514/V300074223_L03_514 | None |
| Sample code | SB04.05C1a | None |
| Sequencing company | BGI | None |
| Marker | Measurement | Units |
|---|---|---|
| Treatment code | Saturn | None |
| Treatment concentration | 4.4% | % |
| Treatment description | Sanford Blue Mussel Meal | None |
| Marker | Measurement | Units |
|---|---|---|
| Environment | Tanks (flow-through) | None |
| Trial code | SB | None |
| Trial description | Trial B: Blue mussel-dose response | None |
| Trial end | 2019-11-22 | None |
| Trial start | 2019-08-14 | None |
Sample SAMEA8141778 may have been analysed by MGnify. Lookup sample on MGnify
| Analysis accession | Run/assembly accession | MGnify pipeline version | Experiment type | Detail |
|---|
No analyses found in MGnify
Sample SAMEA8141778 has nucleotide sequencing data in the European Nucleotide Archive (ENA): 162,123,377bp sequenced by 1,089,626 reads. View sample SAMEA8141778 in ENA
| Data domain | Accession | Title/alias |
|---|---|---|
| Sample | SAMEA8141778 | SB04.05C1a |
| Reads (Run) | ERR5376960 | webin-reads-SB04_05C1a_metaT |
| Reads (Experiment) | ERX5162067 | Illumina NovaSeq 6000 sequencing: Raw reads: SB04_05C1a_metaT |
| Project/Study | PRJEB43098 | HoloFood Salmon Trial A+B Gut Metatranscriptome |
Documents written by HoloFood partners and collaborators relevant to Sample SAMEA8141778