Data

Data from Manuscripts

Bertrand_et_al_PNAS_2015_Fig2

  • Dupont, Chris L. and McCrow, John P. and Valas, Ruben and Moustafa, Ahmed and Walworth, Nathan and Goodenough, Ursula and Roth, Robyn and Hogle, Shane L and Bai, Jing and Johnson, Zackary I. and Mann, Elizabeth and Palenik, Brian and Barbeau, Katherine A. and Craig Venter, J. and Allen, Andrew E. 2015. Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. ISME J. 9:1076-1092. : International Society for Microbial Ecology 10.1038/ismej.2014.198
    • Pelagomonas sp. CCMP1756 transcriptome and contigs, nucleotides and amino acids for predicted peptides and annotation of Sanger and 454 metagenomic data and total and polyadenylated RNA metatranscriptomic data can be found here.

Dupont_et_al_ISME_2015_Fig7

  • DÍez, Beatriz and Nylander, Johan A. A. and Ininbergs, Karolina and Dupont, Christopher L. and Allen, Andrew E. and Yooseph, Shibu and Rusch, Douglas B. and Bergman, Birgitta 2016. Metagenomic analysis of the Indian Ocean picocyanobacterial community: Structure, potential function and evolution. PLoS ONE. 11:e0155757. : Public Library of Science 10.1371/journal.pone.0155757
    • Genes encoding Chl-binding proteins and phycobiliproteins can be found here.
  • Kranzler, Chana F., Krause, J.W., Brzenzinski,, M.A., Edwards, B.R., Biggs, W.P., Maniscalco, M., McCrow, J.P., Van Mooy, B.A.S., Bidle, K.D., Allen, A.E., Thamatrakoln, K. 2019. Silicon limitation facilitates virus infection and mortality of diatoms
    • Unassembled reads and rRNA data from this study can be found here
    • Assembled contigs can be found here
  • Kolody, B., McCrow, J., Zeigler-Allen, L., Aylward, F., Fontanez, K., Moustafa, A., Moniruzzaman, M., Chavez, F., Scholin, C., Allen,E., Worden, A., DeLong, E.F., Allen, A.E.  Diel  transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection
    • Unassembled reads and rRNA data from this study can be found here
    • Assembled contigs, ORFs, and annotation can be found here here

 

Databases and Collections

1. PhyloDB 1.075. PhyloDB is custom database suitable for comprehensive annotation of metagenomics and metatranscriptomics data. It is comprised of peptides obtained from KEGG, GenBank, JGI, ENSEMBL, and various other repositories. Version 1.075 of the database consists of 24,509,327 peptides from 19,962 viral, 230 archaeal, 4910 bacterial, and 894 eukaryotic taxa. The database also contains all data from the Marine Microbial Eukaryotic Transcriptome Sequencing Project which is represented by 8,807,335 peptides from 409 taxa.

2. Marine Microbial Eukaryotic Transcriptome Sequence Project (MMETSP).

MMETSP metadata, contgs, nucleotides and amino acids from predicted proteins and associated annotation and expression spreadsheets for each of the 410 singleton or combined assemblies can be found here.

Phylo-METAREP provides a suite of high-performance web based tools to view, query, browse and compare annotated transcriptomes in real time. Phylo-METAREP can be accessed with username and password GUEST. For Phylo-Metarep source code and installation information please visit our the Allen Lab GitHub page.

3. NOAA CalCOFI Genomics Project (NCOG)

The NOAA-California Cooperative Oceanic Fisheries Investigations (CalCOFI) Ocean Genomics (NCOG) Project employs genome-based ocean assessments to complement and augment observations currently collected in the CalCOFI, California Current Ecosystem Long Term Ecological Research (CCE-LTER), and Southern California Coastal Observing System (SCCOOS) programs.

4. Other microbial diversity data sets