Data · dataset · 2014
Marine microbial eukaryote transcriptomes
Listed in DataCite
Description
Overview This repository provides assemblies of a sub-set publicly available short read (Illumina 50bp PE) datasets of marine microbial eukaryotes. The raw data were generated by the Marine Microbial Eukaryote Transcriptome Sequencing Project (marinemicroeukaryotes.org/). This project provides its own set of assemblies (generated using the Abyss assembler).
Since our work-flows are geared towards assemblies generated by the Trinity assembler, raw data were obtained from the following website marinemicroeukaryotes.org/ and assembled using Trinity (trinityrnaseq.sourceforge.net/) For our purposes the raw data were directly assembled using Trinity (see README for version number) using the default settings. Several species/strains were assembled using all available Illumina libraries combined (see README).
Read the rest (3 more)
The identifiers of the raw data are provided and culture conditions of the organisms can be retrieved from marinemicroeukaryotes.org/ using the MMETSP ID (see README for list). If you use these data please cite Keeling, P.J. et al., 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing.
PLoS Biology, 12:e1001889. Grabherr, M.G. et al., 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Nature Biotechnology, 29:644-652. Funding NSF Dimensions of Biodiversity Grant DEB-1046075
Links
Where it is published
- Repository landing page figshare.com/articles/dataset/Marine_microbial_eukaryote_transcriptomes/115… ↗
landing page · from DataCite
- DOI doi.org/10.6084/m9.figshare.1152727 ↗
DOI / persistent id · from DataCite
Documentation and papers
Catalogue records · 2
- DataCite API api.datacite.org/dois/10.6084/m9.figshare.1152727 ↗
metadata API · from DataCite
- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.1152727 ↗
catalogue entry · from DataCite
Topics
- Stated by source
- Biological sciences
- From keywords
- Biochemistry and cell biology · Microbiology · Plant biology
- Inferred from text
- RNA sequencing 65% · Sequencing 75%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DataCite | 10.6084/m9.figshare.1152727 | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| byte_size | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].fos:biological-sciences | source · DataCite | connector:datacite@1.0.0 | |
| concepts[modality].local:modality:rna-seq | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:sequencing | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · DataCite | connector:datacite@1.0.0 | |
| description | source · DataCite | connector:datacite@1.0.0 | /data/attributes/descriptions |
| license | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| publication_date | source · DataCite | connector:datacite@1.0.0 | /data/attributes/dates |
| title | source · DataCite | connector:datacite@1.0.0 | /data/attributes/titles/0/title |
| updated_date | source · DataCite | connector:datacite@1.0.0 |