Data files
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Pteridines checked for Pan-assay interference compounds with the FAF-Drugs4 webserver (https://fafdrugs4.rpbs.univ-paris-diderot.fr/, last checked August 2020 and Lagorce et al. (2015) Nucleic Acids Res. 43, W200–207). Archive of PAINS filtering and ADME-Tox prediction results from FAF-Drugs4 run performed April 2019 with compound SMILES as input: applied_filters.txt: list of filters used; compound.sdf, accepted.sdf, intermediate.sdf, rejected.sdf, covalent_inhibitors.sdf and pains.sdf: compound ...
Creator: Ina Poehner
Submitter: Ina Poehner
Creator: Fatemeh Zamanzad Ghavidel
Submitter: Fatemeh Zamanzad Ghavidel
Results of gas chromatography of fatty acid composition of feeds used in Study "GSF1: Salmon feed-switch experiment vegetable and fish oil 2015-2016", https://fairdomhub.org/studies/144.
Feed samples are identified by their EWOS feed number. Fatty acids are identified by ChEBI ID. Numbers in table are mass percentage of lipid fraction.
Details on recipes, pellet size etc for each feed ID are in https://fairdomhub.org/data_files/1308.
(The above clarifications required some detective work, which ...
Creators: Jon Olav Vik, Magny Sidsel Thomassen, Graceline Tina Kirubakaran
Submitter: Jon Olav Vik
This is the fatty acid profile data from the freshwater portion of the feed switch trial. The last column has the sample ID eg: D0_MA-L-1/9_6 (Day 0, MA- Marine oil, L-liver, 1/9 sept 1, fish number 6
Fatty acid Systematic Name C14:0 Myristic acid myristin-syre C16:0 Palmitic acid palmitin-syre C16:1n7 Palmitoleic palmitolein-syre C17:0 C17:1 C18:0 stearic acid stearin-syre 18:1n9c oleic acid olje-syre C18:2n6c linoleic acid linolsyre C20:1 eicosenoic acid C18:3n3 linolenic acid linolensyre C20:2 ...
Creators: Graceline Tina Kirubakaran, Inga Leena Angell, Thomas Harvey, Jon Olav Vik, Magny Sidsel Thomassen
Submitter: Graceline Tina Kirubakaran
Fatty acid Systematic Name
C14:0 Myristic acid myristin-syre C16:0 Palmitic acid palmitin-syre C16:1n7 Palmitoleic palmitolein-syre C17:0 C17:1 C18:0 stearic acid stearin-syre 18:1n9c oleic acid olje-syre C18:2n6c linoleic acid linolsyre C20:1 eicosenoic acid C18:3n3 linolenic acid linolensyre C20:2 eicosadienoic C22:1 cetoleic acid cetolein-syre C20:3n3 eicosatrienoic acid C20:4n6 arachidonic acid arakidon-syre ARA C22:2 C20:5n3 eicosapentaenoic acid EPA C24:1 nervonic acid C22:5n3 docosapentaenoic ...
Creators: Thomas Harvey, Magny Sidsel Thomassen
Submitter: Thomas Harvey
FBA result of flux distribution in butanol producing e.coli strain, which designed using RobOKoD.
Creator: Natalie Stanford
Submitter: Natalie Stanford
Kinetic characterisation of FBPAase. Expermental data for enzyme reaction rates with increasing concentrations of DHAP and GAP.
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Simulation results of FBPAase of experimental data for DHAP and GAP saturation
Creator: Jacky Snoep
Submitter: Jacky Snoep
_p_RNAinVAL/_I_01_LabTrials/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/
Creator: Marko Petek
Submitter: Marko Petek
The file contains FeaturePlots of 4 different cardiomyocyte markers (Actn2, Tnnc1, Actc1 and Ryr2) to demonstrate how annotation of clusters needs to be based on several markers and approaches, which in the aggregate allow for more reliable conclusions/results.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
FASTA file of representative sequences for operational taxonomic units in gut microbiota analyses from feed-switch experiment at Solbergstrand Sept 2015.
(Knut Rudi --> Jon Olav Vik 20160126, email subject "metadata for alle fisk".)
File contents look like this:
OTU_1 1..446 -GTCC---GCCCTACGGGAT... OTU_2 1..446 -GTCC--GCCC-TACGGGAT... ... OTU_439 1..472 ----ATGTCACCTACGGGAT...
Creators: Jon Olav Vik, Knut Rudi
Submitter: Jon Olav Vik
Gut microbiota analysis of the fish whose gross phenotypes are listed in https://fairdomhub.org/data_files/1244. Besides identification of the fish, the data are a 130 x 435 matrix showing amounts of operational taxonomic units (OTUs), one row per fish and one column per OTU (https://en.wikipedia.org/wiki/Operational_taxonomic_unit). Sequences that characterize each OTU are in https://fairdomhub.org/data_files/1317. Amounts are measured as the number out of 2000 sequences examined that contain a ...
Creators: Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran, Sahar Hassani
Submitter: Inga Leena Angell
Path to this file: orion:~jonvi/genosysfat/SRS_lakselever_pilot.sf3 Attempt at workaround because the "Remote URL" field only accepts http, https, ftp: ftp://10.209.0.221/mnt/users/jonvi/genosysfat/SRS_lakselever_pilot.sf3
This file resides on the "orion" server (currently 10.209.0.221) at Cigene, which is only reachable from within NMBU network, e.g. via vpn.nmbu.no (as username@nmbu.no).
It is a 190 MB binary file to be viewed e.g. by Scaffold, http://www.proteomesoftware.com/products/scaffold/download. ...
Creators: Jon Olav Vik, Morten Skaugen, Simen Rød Sandve
Submitter: Jon Olav Vik
List of 40 proteins as targets for pilot proteomics analysis of feed-switch samples (of liver, I presume).
E-mail from Simen Rød Sandve to Morten Skaugen 2015-08-11:
On Tue, Aug 11, 2015 at 10:01 AM, Simen Rød Sandve wrote: Please find attached an excel table with 40 proteins of interest (names, annotation, and protein sequence). I know we mentioned 20 proteins as a nice number to aim for in the targeted analyses – but we couldn't really seem to agree on a smaller subset . Please see if its ...
Creators: Jon Olav Vik, Simen Rød Sandve
Submitter: Jon Olav Vik
Spreadsheet 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")
...
Creators: Jon Olav Vik, Jacob Seilø Torgersen, Arne Gjuvsland, Sandve Simen, Yang Jin, Tom Harvey
Submitter: Jon Olav Vik
FASTA file of representative sequences for operational taxonomic units in gut microbiota analyses from feed-switch experiment at Solbergstrand January 2016.
Creators: Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran, Sahar Hassani
Submitter: Inga Leena Angell
Gut microbiota analysis of fish sampled in january 2016. The data is found in row 335-548 and downwards (Sheet 1). The first 16 colums contain information about the fish, and the following columns (From R to AJO) each represent an OTU (Operational taxonomic unit) with the given taxonomy for each OTU presented in the bottom row. Sequencing depth was kept at 13000 sequences per sample, thus the numbers presented in the OTU columns represent the number of sequences matching the specific OTU from the ...
Creators: Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran, Sahar Hassani
Submitter: Inga Leena Angell
Creator: Thomas Rimpf
Submitter: Thomas Rimpf
Creator: Thomas Rimpf
Submitter: Thomas Rimpf
Creator: Thomas Rimpf
Submitter: Thomas Rimpf
Creator: Thomas Rimpf
Submitter: Thomas Rimpf
acetic acid addition 70mM
Creator: Sebastian Curth
Submitter: Sebastian Curth
pulse acetic acid: 70mM (2x), 80mM, shift to 4.5, pulse acetic acid: 70mM
Creator: Sebastian Curth
Submitter: Sebastian Curth
acetic acid addition
step experiment: 50mM, 70mM, 100mM, 120mM
pulse 200mM
Creator: Sebastian Curth
Submitter: Sebastian Curth
acetic acid pulse 100mM acetic acid step 50mM, 70mM
Creator: Sebastian Curth
Submitter: Sebastian Curth
Creator: Thomas Rimpf
Submitter: Thomas Rimpf
Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel
Submitter: Jay Moore
Creators: David Rand, R Jansen, Maria Elena Merlo, Morris Swertz, Preben Krabben, Kay Nieselt, Wolfgang Wohlleben, Jens Reuther, David Hodgson, Anthony Palathingal, David Wild, Elizabeth Wellington, Gregory Challis, Nigel Burroughs, Walid Omara, William Gaze, Brent Kiernan, Roxane Legaie, Sunniva Hoel, Juan-Francisco Martin, Antonio Rodríguez-García, Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Jay Moore, Alexander Wentzel, Maggie Smith, Louise Thomas, Eriko Takano, Lubbert Dijkhuizen, Rainer Breitling, M. Tauqeer Alam
Submitter: Jay Moore
Proteomics from MCADD and control individuals' fibroblasts.
Creators: Christoff Odendaal, Barbara Bakker, Emmalie Jager, Terry G.J. Derks, Karin Wolters; Anne-Claire Martines
Submitter: Christoff Odendaal
Data file for PLaSMo accesssion ID PLM_64, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_64, version 3
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_64, version 4
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_64, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_64, version 3
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_64, version 4
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Creator: Dorothee Houry
Submitter: Dorothee Houry
Data file for PLaSMo accesssion ID PLM_9, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Creator: Runyu Liang
Submitter: Runyu Liang
Creator: Runyu Liang
Submitter: Runyu Liang
Creator: Runyu Liang
Submitter: Runyu Liang
Creator: Runyu Liang
Submitter: Runyu Liang
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Runyu Liang
Submitter: Runyu Liang
Creator: Runyu Liang
Submitter: Runyu Liang
Creator: Runyu Liang
Submitter: Runyu Liang
This pdf file contains all figures of the article "Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mice" in high resolution.
Creators: Anne-Marie Galow, Markus Wolfien
Submitter: Anne-Marie Galow
Information connecting RNA seq fastq-files to corresponding fish ID/exposure regime
Creators: Karina Dale, Pål A. Olsvik
Submitter: Karina Dale
Data file for PLaSMo accesssion ID PLM_30, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
This .csv file contains the filtered datset of the anaerobic to aerobic transition. Values are shown if they show a statistically significant change relative to the 0 minute transcriptional profile (t-test p<0.05 and 2-fold cut-off).
Creator: Matthew Rolfe
Submitter: The JERM Harvester
This .csv file contains the filtered datset of the aerobic to anaerobic transition. Values are shown if they show a statistically significant change relative to the 0 minute transcriptional profile (t-test p<0.05 and 2-fold cut-off).
Creator: Matthew Rolfe
Submitter: The JERM Harvester
Very simple unrealistic values for Fisetin kinetics (Km). For use in a simple graphical model.
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
This data contains fish data such as fish abundance, fish community structure data, fish species data obtained in the study, fish productivity and also fish length-weight relationships.
Creator: Andi N.K.B.P Iskandar
Submitter: Andi N.K.B.P Iskandar
Microarray data at end of day (ED) and end of night (EN) in 4, 6, 8, 12, and 18h photoperiods.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Creators: Daniel Seaton, Andrew Millar
Submitter: Daniel Seaton
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Excel sheet contains:
- flux distribution solution from best iteration cluster
- quality of the fit (experimental MIDs vs. simulated MIDs)
- Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach
Creator: Michael Kohlstedt
Submitter: Michael Kohlstedt
Excel sheet contains:
- flux distribution solution from best iteration cluster
- quality of the fit (experimental MIDs vs. simulated MIDs)
- Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach
Creator: Michael Kohlstedt
Submitter: Michael Kohlstedt
Excel sheet contains:
- flux distribution solution from best iteration cluster
- quality of the fit (experimental MIDs vs. simulated MIDs)
- Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach
Creator: Michael Kohlstedt
Submitter: Michael Kohlstedt
This .csv file shows FNR activity at different aerobiosis levels
Columns a_old Desired aerobiosis level (Aerobiosis units or %AAU) Bgal_activity Average FNR reporter activity (Miller units) Bgal_STDEV STDEV of FNR reporter activities (Miller units) rDOT(μM) Dissolved oxygen tension (μM) DCW DCW (g/L) [acetate] Extracellular acetate concentration (mM) Qacetate Acetate flux (mmoles/h/gDCW) a_new Actual aerobiosis level in sampled chemostat
Creator: Matthew Rolfe
Submitter: The JERM Harvester
A .pdf files showing graphs of FNR activity at varying aerobiosis levels
Top graph shows no acetate re-calibration Bottom graph shows data with acetate re-calibration
Creator: Matthew Rolfe
Submitter: The JERM Harvester
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/
Creator: Marko Petek
Submitter: Marko Petek
Excel workbook with included Read.Me sheet, including FW and DW biomass data derived from files linked elsewhere; a compilation of the rosette area and gas exchange data for every plant measured of the Col, lsf1 and prr7prr9 genotypes; statistical analysis across the experiments; and charts of the compiled data, some of which are presented as figure panels in the 2022 versions.
Creators: Yin Hoon Chew, Andrew Millar
Submitter: Andrew Millar
Summary of fragments that were used to construct an in silico pteridine library with corresponding fragment identifiers. Connections between the fragments are shown outside the colored boxes. Compounds were composed of a core fragment (C1-C3), an N10 fragment (N1-N7), a PABA fragment (P1-P10) and, for any PABA fragment except P8, P9 and P10, a tail fragment (T1E1-T7).
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq
Creators: Fabian Grammes, Yang Jin
Submitter: Sahar Hassani
Data file for PLaSMo accesssion ID PLM_6, version 1
Creators: BioData SynthSys, Alexandra Pokhilko, Andrew Millar
Submitter: BioData SynthSys
- Summary of functional categorization of all identified proteins of P. cordatum
- Calculations of general functions (Fig. 5, left panel)
- Calculations of nuclear functions (Fig. 5, right panel)
- Categories in separate sheets
Tab color: Summarized data, purple; calculations, organge; functional categories, green
Creators: None
Submitter: Jana Kalvelage
Link to the repository for functional annotation
Creator: Malte Herold
Submitter: Malte Herold
Additional data for the calculations and proteomic dataset of the catabolsim of P. vulgatus containing:
- Genome
- Proteomic data of the pathways and respiration
- Proteomic data of the transporter
- Proteomic data of the sus-like system
- Calculation of the cell dry weight and total cell count
- Calculations of the specific ATP yield
- Calculations of the product yields and biomass yields
Creators: Urte Clausen, Sören-Tobias Vital
Submitter: Urte Clausen