Data Collections

Isolate Transcriptomes: Transcriptomes from our culture collection are deposited in Cyverse under the project name unc_phyto_isolates. They can be accessed via the Cyverse Discovery Environment or Data Commons.

Data From Publications

Cohen NR, Gong W, Moran DM, Mclivin MR, Saito M and Marchetti A. (2018) Transcriptomic and proteomic responses of the oceanic diatom Pseudo-nitzschia granii to iron limitation. Environmental Microbiology. doi.org/10.1111/1462-2920.14386.

Download assembled Pseudo-nitzschia granii contigs, raw read counts, and KEGG annotations here.

 

Lampe RH, Cohen NR, Ellis KA, Bruland KW, Maldonado MT, Peterson TD, Till CP, Brzezinski MA, Bargu S, Thamatrakoln K, Kuzminov FI, Twining BS, and Marchetti A. (2018) Divergent gene expression among phytoplankton taxa in response to upwelling.

Raw reads are deposited in SRA: BioProject PRJNA320398
Contigs, counts, and annotations are deposited in Zenodo: DOI

 

Gong W, Paerl H, and Marchetti A (2018). Eukaryotic phytoplankton community spatiotemporal dynamics as identified through gene expression within a eutrophic estuary. Environmental Microbiology.

Dataset 1: Assembled contigs for metatranscriptomic libraries
Dataset 2: Final composite dataset including a list of contigs with associated functional and taxonomical annotations as well as quantitative read counts.

Download datasets here.

 

Cohen NR, Ellis KA, Lampe RH, McNair H, Twining BS, Maldonado MT, Brzezinski MA, Kuzminov FI, Thamatrakoln K, Till CP, Bruland KW, Sunda W, Bargu S, Marchetti A. (2017) Diatom transcriptional and physiological responses to changes in iron bioavailability across ocean provinces. Frontiers in Marine Science. doi: 10.3389/fmars.2017.00360.

Download metafiles here.

 

Cohen NR, Ellis KA, Burns WG, Lampe RH, Schuback N, Johnson Z, Sañudo-Wilhelmy S, and Marchetti A. (2017) Iron and vitamin interactions in marine diatoms of the Northeast Pacific Ocean. Limnology and Oceanography. 10.1002/lno.10552.

Download contigs, counts, and annotations here.

 

Gong W, Browne J, Hall N, Schruth D, Paerl H, and Marchetti A. (2017) Molecular insights into a dinoflagellate bloom. ISME Journal. 11. 439-452.

Manually curated taxonomic lookup table: table2_taxonomy_lookup

Dataset 1: Assembled contigs for the bloom and non-bloom stations sequence libraries
Dataset 2: Differential expression analysis results for: bloom vs station 20, bloom vs station 70 and station 20 vs station 70
Dataset 3: Final composite dataset including a list of contigs with associated functional and taxonomical annotations as well as quantitative read counts
Dataset 4: Normalized counts at KO level in the bloom and non-bloom stations

Download datasets here.