Could not connect to MGnify right now. Please try later.
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 SAMEA112642744, a HoloFood metagenomic-amplicon salmon sample
Metadata for sample SAMEA112642744, 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 | SAMEA112642744 | 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 | ERS14634713 | None |
| Submitter Id | SA05_03C1a_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 SA05.03 from tank SA05 with treatment Cougar | 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 | Cougar SA Seaweed 1.5% | None |
| host diet treatment concentration | 0 | % mass |
| host disease status | Wounded:- | None |
| host gutted mass | 233.6 | g |
| host length | 25.5 | cm |
| host scientific name | Salmo salar | None |
| host storage container | LetSea Tank: Cougar | None |
| host storage container pH | 7.05 | None |
| host storage container temperature | 12.76 | °C |
| host subject id | SA05.03 | None |
| host taxid | 8030 | None |
| host total mass | 278.8 | 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 | SA05.03C1a | 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 | LPS00563 | None |
| Omics | Metagenomics | None |
| Organism | Salmon | None |
| Pool | S-MG-P39-530 | None |
| Project | HoloFood | None |
| Raw seq. name | S-MG-P39-530/V300074241_L03_530 | None |
| Sample code | SA05.03C1a | None |
| Sequencing company | BGI | None |
| Marker | Measurement | Units |
|---|---|---|
| Treatment code | Cougar | None |
| Treatment concentration | 1.5% | % |
| 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 SAMEA112642744 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 SAMEA112642744 has nucleotide sequencing data in the European Nucleotide Archive (ENA): 44,505,349bp sequenced by 183,442 reads. View sample SAMEA112642744 in ENA
| Data domain | Accession | Title/alias |
|---|---|---|
| Sample | SAMEA112642744 | SA05.03C1a |
| Reads (Run) | ERR10888885 | webin-reads-SA05_03C1a_16S |
| Reads (Experiment) | ERX10332899 | Illumina MiSeq sequencing: Raw reads: SA05_03C1a_16S |
| Project/Study | PRJEB59908 | Holofood Salmon 16S amplicon sequencing |
Documents written by HoloFood partners and collaborators relevant to Sample SAMEA112642744