831fa9bbcd9d6bb3c6d8fca5400a10a1 English dataset Data Archive for Seabed Species and Habitats (DASSH) Data Manager 01752 633102 01752 633291 Marine Biological Association of the UK, The Laboratory, Citadel Hill Plymouth PL1 2PB dassh.enquiries@mba.ac.uk pointOfContact 2024-05-21 MEDIN Discovery metadata standard 2.3.8 urn:ogc:def:crs:EPSG::4326 2020, Glen Wheeler, The Marine Biological Association of the UK (MBA) Coccolithus braarudii life cycle protein mass spectrometry 2024-02-01 publication 2021-04-01 creation 2021-04-01 revision DASSHDT00000529 http://dassh.ac.uk Coccolithophores are crucial for marine biogeochemical cycling. However, much of their physiology remains poorly understood, particularly their elusive haplo-diplontic life cycle. We aimed to characterise differences between HET and HOL Coccolithus braarudii by carrying out protein mass spectrometry of both life phases. We found that the proteome was substantially different and characterized novel physiological mechanisms. Daniela Sturm Marine Biological Association of the United Kingdom danstu@mba.ac.uk originator Data Archive for Seabed Species and Habitats (DASSH) Data Manager 01752 633102 01752 633291 Marine Biological Association of the UK, The Laboratory, Citadel Hill Plymouth PL1 2PB dassh.enquiries@mba.ac.uk custodian notPlanned Delimited Marine Environmental Data and Information Network NDGO0005 Species distribution GEMET - INSPIRE themes, version 1.0 2008-01-06 revision Biodiversity GEMET 2011-07-06 creation Phytoplankton generic abundance in water bodies SeaDataNet P021 parameter discovery vocabulary 2009-11-16 revision CC BY otherRestrictions open access English biota -4.1398 -4.1382 50.3638 50.3647 2020-07-01 2021-04-01 Data Archive for Seabed Species and Habitats (DASSH) Data Manager 01752 633102 01752 633291 Marine Biological Association of the UK, The Laboratory, Citadel Hill Plymouth PL1 2PB dassh.enquiries@mba.ac.uk distributor http://doi.org/10.17031/65afd01b4e0e2.1 DOI link A link to the web service or dataset http://www.dassh.ac.uk DASSH Website A link to the general host site dataset Coccolithophore culturing, harvesting, and protein extraction - Haploid and diploid cultures of C. braarudii were cultured at 15 degrees celsius and harvested during mid-exponential growth. Proteins were extracted using RIPA buffer and liquid nitrogen grinding. Coccolithophore protein mass spectrometry (MS) - TMT labelling, Liquid Chromatography Mass Spectrometry and subsequent raw data analysis were carried out by the Proteomics Facility of Bristol University, UK. The raw data files were processed and quantified using Proteome Discoverer software v2.1 (Thermo Scientific) and searched against the latest release version 2021_2 of the C. braarudii predicted protein database (25204 proteins) from Uniprot (www.uniprot.org), and a common contaminates database using the SEQUEST HT algorithm. The reverse database search option was enabled, and all data was filtered to satisfy false discovery rate (FDR) of 5 percent, which is classed as FDR confidence = Medium. Data were normalized to the total peptide amount in each sample by Proteome Discoverer to equalize peptide abundances across all TMT channels and correcting for differences in sample loading. Normalized proteins were subsequently quality controlled. Differential abundance between life phases was assessed using LIMMA (Ritchie et al., 2015), with a significance level of less than 0.05. Notes on the data spreadsheet - Accession: Uniprot Accession Number for Coccolithus braarudii logFC, AveExpr, t, P.Value, adj.P.Val, B - For information on analysing RNAseq or protein MS data, see package LIMMA: https://kasperdanielhansen.github.io/genbioconductor/html/limma.html Unique Peptides - Number of unique peptide for each protein Protein FDR Confidence: False discovery rate (FDR), 5 percent = Medium, 1 percent = High Blast2GO - Protein annotation Description - Protein description from Uniprot Best BLAST hit and e value: NCBI Blast hit with highest e-value