Feed switch 2015-09, 2016-01 Solbergstranda gross phenotypes
ExploreSpreadsheet of weight, length and sex of fish sampled after feed switch between vegetable and marine oil, in September 2015 (freshwater) and January 2016 (seawater).
Spreadsheet columns are:
- Date (YYYY-MM-DD)
- Day (day zero is the day before first feeding with new feed)
- Inputter (person entering data into Excel)
- Tank (1, 2, 4, 5 with Atlantic salmon, 3 and 6 with rainbow trout)
- Section (tanks were divided in half using perforated walls)
- Treatment (explained in sheet "treatments")
- Species
- Fish # (in the spreadsheet, fish are numbered within tank-sections for Sept 2015 and within treatments for Jan 2016. I suspect the sample tubes were numbered within treatments even for Sept 2015)
- Weight g
- Length mm
- Start cutting (approximate time of day, and only sporadically registered)
- Sex (male, female)
- Notes (free text)
- End freezing (time of day, sporadically registered)
- Duration (computed from time-points if registered)
- "Tube label (X = tissue: G=gut, L=liver, M=muscle)" (e.g. D1-M->V-X-3/9#1 for 2015 and D20_MA_VO_X_T2-5 for 2016, see https://fairdomhub.org/sops/248
- Life stage (FW = freshwater, SW = saltwater)
- Fish number (1, 2, ..., 549, and one called 999 which was discovered in the freezer years later). Unique within the GSF1 experiment. If at all possible, use this as your primary key when processing the data, possibly in conjunction with tissue type: M123 etc.
- Sample ID stem: e.g. GSF1_SW_D20_VOMA_F546 means "GSF1 experiment, SW life stage, Day 20, vegetable-oil-to-marine diet switch, fish number 546".
- G, L, M: Tissue sample identifiers for gut, liver, muscle (appending
_G,_L,_M). These turned out to be too long for some applications, so our recommendation is now to use M123 etc, seeFish numberabove. - RNAseq FG id: Identifiers used by Fabian Grammes for RNAseq data. Generated as documented in https://gist.github.com/jonovik/62f0216e7fae39e34305ea0eda049ca3.
The sheet "sanity checks" contains pivot tables of number of fish sampled per day, tank, section, treatment etc. The sheet "RNAseq ID from Version 3" contains a copy of Version 3, with fish numbers (F-numbers) added for lookup.
Version 2 is also on Bitbucket as
https://bitbucket.org/cigenebb/genosysfat/src/9b764bc/genosysfat%20sampling%20solbergstranda%202015-09,%202016-01.xlsx.
Version 3 was generated as per https://gist.github.com/jonovik/62f0216e7fae39e34305ea0eda049ca3.
Version 4 is essentially a revert to Version 2 but merging in RNAseq identifiers from Version 3.
Version 5 adds a fish discovered in the freezer in 2021 when preparing for GSF1-RNA-2021 (Experimental Assay).
Version 6 maps sample identifiers from 2016 RNA-seq https://fairdomhub.org/assays/352 to fish identifiers used here.
SEEK ID: https://fairdomhub.org/data_files/1330?version=6
Filename:
genosysfat sampling solbergstranda 2015-09 2016-01 Version 6.xlsx
Format: Spreadsheet
Size: 260 KB
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Creators and SubmitterCreators
Additional credit
Yang Jin, Tom Harvey
Submitter
Views: 2682 Downloads: 388
Created: 10th Mar 2016 at 20:43
Last updated: 28th Nov 2023 at 12:18
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AttributionsVersion History
Version 6 (latest) Created 28th Sep 2023 at 12:37 by Jon Olav Vik
Map sample identifiers from 2016 RNA-seq https://fairdomhub.org/assays/352 to fish identifiers used here. https://gitlab.com/digisal/rnaseq-muscle/-/blob/0e22cdb/rnaseq-muscle.Rmd#L262-266 There were two "unexpected many-to-many" relationships when linking, but both seem to have a plausible explanation. In one case we found two samples still available while we already had RNA results from one, which probably just means we didn't use a sample for metabolomics. (We did take three replicate liver samples per fish.) In another we have two RNA results from the same fish's liver; it's quite possible we did indeed submit two samples, e.g. because the amount or quality of RNA was small.
Version 5 Created 3rd Jun 2022 at 11:12 by Jon Olav Vik
[Add spreadsheet row for fish discovered in freezer.](https://gitlab.com/digisal/rnaseq-muscle/-/commit/19c0d8bb9330fbdc61fc2614782ccc4bedd0207e)
Version 4 Created 1st May 2018 at 10:16 by Jon Olav Vik
Add easier-to-parse sample identifiers for future use, including metabolomics at NTNU May 2018 onwards. Revert the rest of the spreadsheet to Version 2, but add a sheet from Version 3, which has Fabian Grammes' identifiers used for RNAseq analysis. The script to generate those identifiers is at https://gist.github.com/jonovik/62f0216e7fae39e34305ea0eda049ca3.
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Record of weight, length and sex of fish sampled after feed switch between vegetable and marine oil, in September 2015 (freshwater) and January 2016 (seawater). Young fry arrived at Solbergstranda 2015-02-05 17:20.
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