HoloFood Data Portal
Access samples and data collected and generated by the HoloFood project.
Access samples and data collected and generated by the HoloFood project.
Sample data for SAMEA112642748, a HoloFood metagenomic-amplicon salmon sample
Metadata for sample SAMEA112642748, stored in BioSamples and ENA.
Download all as TSV| Marker | Measurement | Units |
|---|---|---|
| ENA-CHECKLIST | ERC000052 | None |
| ENA-FIRST-PUBLIC | 2023-04-21 | None |
| ENA-LAST-UPDATE | 2023-04-21 | None |
| External Id | SAMEA112642748 | None |
| INSDC center alias | UNIVERSITY OF COPENHAGEN | None |
| INSDC center name | UNIVERSITY OF COPENHAGEN | None |
| INSDC first public | 2023-04-21T12:19:58Z | None |
| INSDC last update | 2023-04-21T12:19:58Z | None |
| INSDC status | public | None |
| SRA accession | ERS14634717 | None |
| Submitter Id | SA06_02C1a_16S | None |
| adapters | AGATCGGAAGAGCACACGTCTGAACTCCAGTCA;AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT | None |
| collection date | 2019-06-11 | None |
| common name | Atlantic salmon | None |
| description | Salmon 16S amplicon sequencing data from Distal gut content; animal SA06.02 from tank SA06 with treatment Tiger | 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 | Fermented algae meal (added in in oil coating) | None |
| host diet treatment | Tiger SA Seaweed 0% | None |
| host diet treatment concentration | 0 | % mass |
| host disease status | Wounded:- | None |
| host gutted mass | 227.2 | g |
| host length | 27 | cm |
| host scientific name | Salmo salar | None |
| host storage container | LetSea Tank: Tiger | None |
| host storage container pH | 7.05 | None |
| host storage container temperature | 12.76 | °C |
| host subject id | SA06.02 | None |
| host taxid | 8030 | None |
| host total mass | 265 | g |
| library name | BEST | None |
| library selection | PCR | None |
| nucleic acid extraction | D-rex protocol | None |
| organism | Salmo salar | None |
| pcr primers | N/A | None |
| project | HoloFood | None |
| project name | Holofood Salmon 16S amplicon sequencing | 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 | Salmo salar | None |
| sequencing method | Illumina MiSeq | None |
| title | SA06.02C1a | None |
| trial timepoint | 0 | days |
| Marker | Measurement | Units |
|---|---|---|
| Body site | distal gut content | None |
| Experiment | amplicon | None |
| Index PCR cycles | 12 | None |
| Lab Process ID | LPS00259 | None |
| Omics | Metatranscriptomics | None |
| Organism | Salmon | None |
| Pool | SA06_02_MT | None |
| Project | HoloFood | None |
| Raw seq. name | X204SC20112698-Z02-F005/raw_data/SA06_02_MT | None |
| Sample code | SA06.02C1a | None |
| Sequencing company | Novogen | None |
| Marker | Measurement | Units |
|---|---|---|
| Treatment code | Tiger | None |
| Treatment concentration | 0.0% | % |
| Treatment description | Fermented algae meal (added in in oil coating) | None |
| Marker | Measurement | Units |
|---|---|---|
| Environment | Tanks (flow-through) | None |
| Trial code | SA | None |
| Trial description | Trial A: Seaweed-dose response | None |
| Trial end | 2019-08-13 | None |
| Trial start | 2019-06-11 | None |
Sample SAMEA112642748 may have been analysed by MGnify. Lookup sample on MGnify
| Analysis accession | Run/assembly accession | MGnify pipeline version | Experiment type | Detail |
|---|---|---|---|---|
| MGYA00637119 | ERR10888859 | 5.0 | amplicon | View on MGnify |
Sample SAMEA112642748 has nucleotide sequencing data in the European Nucleotide Archive (ENA): 7,807,773bp sequenced by 32,224 reads. View sample SAMEA112642748 in ENA
| Data domain | Accession | Title/alias |
|---|---|---|
| Sample | SAMEA112642748 | SA06.02C1a |
| Reads (Run) | ERR10888859 | webin-reads-SA06_02C1a_16S |
| Reads (Experiment) | ERX10332873 | Illumina MiSeq sequencing: Raw reads: SA06_02C1a_16S |
| Project/Study | PRJEB59908 | Holofood Salmon 16S amplicon sequencing |
Documents written by HoloFood partners and collaborators relevant to Sample SAMEA112642748
