Data · dataset · 2025
Data for Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis
Listed in Teesside University Research Data Repository
Raw data files used in the analyses for the in-prep 2024 manuscript Genomes of nitrogen-fixing eukaryotes reveal a non-canonical model of organellogenesis .
Description
Summary below File descriptions: Genome files: Ep = E. pelagica, Ec = E. clementina. E. pelagica genome assembly is previously published and available at GCA_946965045.2, all E. pelagica files are compatible with the NCBI files.
The diazoplast of E. clementina was previously published at GCA_029919255.1 [diatom].gtf de novo annotation feature file [diatom].faa translation of annotation feature file Ec.nuc.fasta nuclear genome of E. clementina Ec. mito.fasta mitochondrial genome of E. clementina Ec.chlo.fasta chloroplast genome of E. clementina Figure 1: 1A_SpeciesAccessions.xlsx All accessions for sequences 1C_[diatom].masked.comparative.summary.tbl Output tables form the denovo repeatmasker run. 1D_Pairwise percent identity.csv All pairwise % amino acid identity values of protein orthologues between species pairs 1E_DiatomOrthogroups.xlsx Orthogroups and genes within them (orthofinder Orthogroups.tsv file) 1E_Orthogroup_overlap_and_percent_identity_statistics.csv Pairwise % identity of protein orthologues and jaccard index of the overlap between orthogroups 1E_Individual_orthogroup_membership.csv Orthogroups and number of genes for each species contained within them (orthofinder Orthogroups.GeneCount.tsv file) 1E_HGTRawResults.xlsx Output of HGT search for all diatoms.
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The result fields include, HGT confidence based on tree topology, AI score, and top blast hit taxa 1E_Ec_HGT_trees.tar.gz Raw phylogenetic trees used to identify HGTs and summary of HGT calls for E. clementina 1E_Ep_HGT_trees.tar.gz As above, for E. pelagica 1E_StudyGeneCodesID.xlsx Table associating the simple gene codes used in the orthogroup analyses in this study to their full corresponding gene IDs on NCBI and other databases Figure 2: 2A_Ec.masked.regions.gff Repeat regions used for genome tracks Figure 4: 4B_4C_ProcessedProteomicsData.xlsx Processed and unprocessed proteomics tables 4B_4C_20230228_orbitrapqexactive_lysate.raw The raw proteomics data from whole cell lysate used for analysis in Figure 5B and C. Run on the orbitrap q-exactive 4B_4C_20231030_orbitrapeclipse_lysate.raw for whole cell lyste, run on the orbitrap eclipse 4B_4C_20230421_orbitrapeclipse_lysate.raw for whole cell lyste, run on the orbitrap eclipse 4B_4C_20231030_orbitrapeclipse_diazo.raw for diazoplast fraction, run on the orbitrap eclipse 4B_4C_20230421_orbitrapeclipse_diazo.raw for diazoplast fraction, run on the orbitrap eclipse 4B_4C_20230228_orbitrapqexactive_diazo.raw for diazoplast fraction, run on the orbitrap q-exactive
Links
Where it is published
- DOI doi.org/10.17632/rr9t3ccbc5.1 ↗
DOI / persistent id · from researchdata tees ac uk
Catalogue records · 1
- OAI-PMH record data.mendeley.com/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Adata… ↗
metadata API · from researchdata tees ac uk
Topics
- From keywords
- Earth & Environmental Science · Engineering · Genomics · Humanities · Life Sciences · Mass spectrometry · Social Science
- Inferred from text
- Tabular 65%
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Teesside University Research Data Repository | oai:data.mendeley.com/rr9t3ccbc5.1 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].anzsrc:field:310509 | mapping · researchdata tees ac uk | vocabulary-mapper@1.0.0 | keywords['Genomics'] |
| concepts[field].local:field:earth-environmental | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:engineering | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:humanities | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[modality].local:modality:mass-spectrometry | mapping · researchdata tees ac uk | vocabulary-mapper@1.0.0 | keywords['Proteomics'] |
| concepts[modality].local:modality:tabular | enrichment · researchdata tees ac uk | keyword-concept-rules@1.0.0 | title+description (65%) |
| description | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/description |
| license | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/rights |
| publication_date | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| title | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/title |