This dataset contains the following:

Metrics databases, as calculated over all pfam and full gene sequences used in this analysis, stored as tab-delimited flat files with headers.- EnsemblGenomes_DomainMetrics.txt.gz: All domain (pfam) metrics calculated from sequences downloaded from ensembl. - EnsemblGenomes_ProteinMetrics.txt.gz: All full gene metrics calculated from sequences downloaded from ensembl.
- NCBIGenomes_DomainMetrics.txt.gz: All domain (pfam) metrics calculated from sequences downloaded from ensembl. - NCBIGenomes_ProteinMetrics.txt.gz: All full gene metrics calculated from sequences downloaded from ensembl.

-S2_SpeciesList:Gives the species, and their reference species UIDs (unique identifier numbers), which are used in the above datatables.

Homology dictionary datasets for each metric. These were created for: ISD, amino acid composition, and hydrophobic clustering. files are organised into a single gzipped folder:
-HomologyDictionaryFiles.zip:

Contents:
Filenames are descriptive, and state: 1) whether the homology groups were calculated over genes or pfams, 2) the metric, 3) whether the data was transformed, 4) over which kingdom the homology groups were calculated over (if any, this is either 'animal' or 'plant'), 5) whether it was specified if the genes or pfams included in the analysis were transmembrane (TransmembraneOnly, or Trans) or not (NonTransmembrane, or NonTrans).
-Filenames starting with 'MetricVsTime: Each file consists of two columns, 'Metric', (as specified in the file title, as either isd, isd without cysteine or clustering), and 'Age', which is the estimated age of the homology group in MY. These are generated by calculating an average over all homologous sequences (either genes or pfams), such that a homologous sequence is only a single datapoint in our analyses. For further details, see manuscript.
-Filenames starting with 'AAComp': Summaries of phylostratigraphy slopes for each amino acid slope

-Files in AACompFiles folder: Each file consists of two columns, 'Metric', (amino acid composition for amino acid specified in file title), and 'Age', which is the estimated age of the homology group in MY. These are generated by calculating an average over all homologous sequences (either genes or pfams), such that a homologous sequence is only a single datapoint in our analyses. For further details, see manuscript.
Sequence data was accessed from Ensembl and NCBI. All scripts used to generate the datasets are available at https://github.com/MaselLab/ProteinEvolution

This dataset contains the following:

Metrics databases, as calculated over all pfam and full gene sequences used in this analysis, stored as tab-delimited flat files with headers.- EnsemblGenomes_DomainMetrics.txt.gz: All domain (pfam) metrics calculated from sequences downloaded from ensembl. - EnsemblGenomes_ProteinMetrics.txt.gz: All full gene metrics calculated from sequences downloaded from ensembl.
- NCBIGenomes_DomainMetrics.txt.gz: All domain (pfam) metrics calculated from sequences downloaded from ensembl. - NCBIGenomes_ProteinMetrics.txt.gz: All full gene metrics calculated from sequences downloaded from ensembl.

-S2_SpeciesList:Gives the species, and their reference species UIDs (unique identifier numbers), which are used in the above datatables.

Homology dictionary datasets for each metric. These were created for: ISD, amino acid composition, and hydrophobic clustering. files are organised into a single gzipped folder:
-HomologyDictionaryFiles.zip:

Contents:
Filenames are descriptive, and state: 1) whether the homology groups were calculated over genes or pfams, 2) the metric, 3) whether the data was transformed, 4) over which kingdom the homology groups were calculated over (if any, this is either 'animal' or 'plant'), 5) whether it was specified if the genes or pfams included in the analysis were transmembrane (TransmembraneOnly, or Trans) or not (NonTransmembrane, or NonTrans).
-Filenames starting with 'MetricVsTime: Each file consists of two columns, 'Metric', (as specified in the file title, as either isd, isd without cysteine or clustering), and 'Age', which is the estimated age of the homology group in MY. These are generated by calculating an average over all homologous sequences (either genes or pfams), such that a homologous sequence is only a single datapoint in our analyses. For further details, see manuscript.
-Filenames starting with 'AAComp': Summaries of phylostratigraphy slopes for each amino acid slope

-Files in AACompFiles folder: Each file consists of two columns, 'Metric', (amino acid composition for amino acid specified in file title), and 'Age', which is the estimated age of the homology group in MY. These are generated by calculating an average over all homologous sequences (either genes or pfams), such that a homologous sequence is only a single datapoint in our analyses. For further details, see manuscript.
Sequence data was accessed from Ensembl and NCBI. All scripts used to generate the datasets are available at https://github.com/MaselLab/ProteinEvolution

Abstract The order (of the discretization error) of a spatial approximation is an important and widely used figure of merit for such approximations. For one-dimensional plane-parallel geometries, it has been shown that most such spatial approximations, as used within the discrete-ordinates directional approximation to monoenergetic particle transport, are instances of the abstract class of closed linear one-cell functional (CLOF) methods. The code LOCFES (Linear One-Cell Functional Experimental Studie... Title of program: LOCFES Catalogue Id: ACJP_v1_0 Nature of problem Monoenergetic and azimuthally symmetric neutron transport in one- dimensional plane-parallel geometry. Versions of this program held in the CPC repository in Mendeley Data ACJP_v1_0; LOCFES; 10.1016/0010-4655(93)90109-P This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)

Abstract The order (of the discretization error) of a spatial approximation is an important and widely used figure of merit for such approximations. For one-dimensional plane-parallel geometries, it has been shown that most such spatial approximations, as used within the discrete-ordinates directional approximation to monoenergetic particle transport, are instances of the abstract class of closed linear one-cell functional (CLOF) methods. The code LOCFES (Linear One-Cell Functional Experimental Studie... Title of program: LOCFES Catalogue Id: ACJP_v1_0 Nature of problem Monoenergetic and azimuthally symmetric neutron transport in one- dimensional plane-parallel geometry. Versions of this program held in the CPC repository in Mendeley Data ACJP_v1_0; LOCFES; 10.1016/0010-4655(93)90109-P This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)

This dataset contains in-situ sensor data from 31 CTD casts (downcast profiles and at upcast bottle firings) collected in the Celtic Sea. The measurements were collected during RRS James Cook cruise JC105 in June 2014, as part of the UK Shelf Sea Biogeochemistry research programme (SSB), in order to provide information on the water mass characteristics and water column structure across the Celtic Sea shelf. Measurements were carried out using a CTD unit that comprised a Sea-Bird Electronics (SBE) 9 plus underwater unit, an SBE 11 plus deck unit, a 24-way SBE 32 carousel and 24 10 L TMF Water Samplers; all of which were mounted on a stainless steel 24-way CTD frame. Attached to the CTD were two SBE 3P temperature sensors, two SBE 4C conductivity sensors, one Paroscientific Digiquartz pressure sensor, one SBE 43 dissolved oxygen sensor, two Chelsea Technology Group (CTG) 2-pi PAR sensors, one WETLabs BBRTD light scattering sensor, one Benthos 916T altimeter one CTG Aquatracka MKIII fluorometer and one CTG Alphatracka MKII transmissometer. This was the instrument set up for the CTD during the entire cruise with the exception of casts 027 and 028, during which the two PAR sensors were not attached to the CTD. Raw data were initially extracted and processed using Seabird Data Processing Software. Modules DatCnv, WildEdit, Filter, AlignCTD, CellTM, Derive and BottleSum were all run. Custom Matlab routines were then used to remove out of water and surface soak values, to filter anomalous data points and to average the profiles onto a 1 db pressure grid. Data were calibrated by comparison with independent samples (where available). Measurements at upcast bottle firings were also calibrated (when possible). The data were collected as part of the SSB research programme in the CaNDyFloSS: Carbon and Nutrient Dynamics and Fluxes over Shelf Systems (NE/K00185X/1) research programme component. SSB was co-funded by the Natural Environment Research Council (NERC) and the Department for Environment, Food and Rural Affairs (Defra). The programme took a holistic approach to the cycling of nutrients and carbon and the controls on primary and secondary production in UK and European shelf seas, to increase understanding of these processes and their role in wider biogeochemical cycles. The British Oceanographic Data Centre (BODC) created the metadata entry and is responsible for holding master copies of the data.

This data set contains sediment characterisation data collected from NIOZ cores in the Celtic Sea across four surveys (DY008, DY021, DY030, DY034) on-board the RRS Discovery (2014-2015). The data were collected at four sampling sites (A, G, H, I) and over a spatial survey carried out on DY021. The author does not have any concerns over the quality of the data set and values are consistent with similar data reported in the wider literature. Samples for sediment characterisation were collected using the NIOZ box corer with 300mm diameter cylindrical barrel. Clear plastic tubes were then inserted into the sediment to collect undisturbed sediment cores for Particle size analysis (PSA)/Organic carbon and Nitrogen (OCN) and syringes with the barrel end cut off were used to collect cores for Rapid fines assessment (RFA) and Porosity/Chlorophyll. All samples were then sliced to known depths. PSA was carried out following the NMBAQC method using a combination of sieve and laser diffraction (Mason 2011). OCN was determined from freeze dried sediment, which was ground and analysed using the Carlo Erba EA1108 Elemental analyser (Kirsten, 1979). RFA was completed through image analysis in Adobe Photoshop CS5 using a novel method (Silburn et. al In Prep). Sediment Chlorophyll samples were freeze dried and a known weight (~0.5g) of dried sediment was extracted in 90% acetone using a modified method of that described by Tett et al (1987). The extracted pigment was then measured using either spectrophotometry (DY008) (HMSO 1980) or fluorescence (DY021, DY030, and DY034) (Tett et al 1987). Porosity samples were weighed, freeze dried and weighed again to get the dry:wet sediment weight ratio (Danielson and Sutherland 1986). Permeability was then calculated from porosity (Engelund 1953). The data were collected as part of the Shelf Sea Biogeochemistry (SSB) research programme as part of the Biogeochemistry, Macronutrient and Carbon Cycling in the benthic layer (BMCC) research programme. SSB was co-funded by the Natural Environment Research Council (NERC) and the Department for Environment, Food and Rural Affairs (Defra). The programme took a holistic approach to the cycling of nutrients and carbon and the controls on primary and secondary production in UK and European shelf seas, to increase understanding of these processes and their role in wider biogeochemical cycles. Sample collection in the field carried out by Briony Silburn, Dave Sivyer, Claire Mason, Paul Nelson, Stefan Bolan (Centre for Environment Fisheries and Aquaculture Science) and Charlie Thompson (Ocean and Earth Science, University of Southampton). The British Oceanographic Data Centre (BODC) created the metadata entry and is responsible for holding master copies of the data.

This dataset contains 105 measurements (99 from CTD rosette, 6 from underway) of seawater dissolved inorganic carbon (DIC) and total alkalinity (TA) from the Celtic Sea (50N, 8W). The samples were collected during RRS James Cook cruise JC105 in June 2014, as part of the UK Shelf Sea Biogeochemistry research programme (UK-SSB), in order to constrain the interior DIC and TA inventories. Measurements were carried out using Apollo SciTech (DIC Analyzer AS-C3 and TA Titrator AS-ALK2) and VINDTA 3C (#024 and #038, Marianda, Germany) instruments at the University of Southampton (UK). Bad results resulting from technical issues during analysis have been removed from these results, so there are no recognised issues. The data were collected as part of the SSB research programme in the CaNDyFloSS: Carbon and Nutrient Dynamics and Fluxes over Shelf Systems (NE/K00185X/1) research programme component. SSB was co-funded by the Natural Environment Research Council (NERC) and the Department for Environment, Food and Rural Affairs (Defra). The programme took a holistic approach to the cycling of nutrients and carbon and the controls on primary and secondary production in UK and European shelf seas, to increase understanding of these processes and their role in wider biogeochemical cycles. The British Oceanographic Data Centre (BODC) created the metadata entry and is responsible for holding master copies of the data.

No description available