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Browsing Research Datasets by Subject "Marine Biology"

Browsing Research Datasets by Subject "Marine Biology"

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  • (16s) No 0. Raw 16S rRNA fastq data files for Bocas hypoxia study 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    This repository contains the <B>RAW</B> sequencing data for hypoxia study. Trimmed reads (with primers removed) are deposited at the European Nucleotide Archive, study accession number <B>PRJEB36632 (ERP119845)</B>.Raw ...
  • (16s) No 1. DADA2 Workflow (16S rRNA) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Output files from the No 1. DADA2 Workflow page of the Bocas Hypoxia study. File names and descriptions:<B>RUN01_read_changes.txt</B>: Tracking changes in read counts (per sample) from the beginning to end of the DADA2 ...
  • (16s) No 2. Data Preparation (16S rRNA) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Output files from the No 2. Data Preparation Workflow page of the Bocas Hypoxia study.File names and descriptions:<B>*seq_table.txt, *_tax_table.txt, *_asv.fasta: </B>Sequence tables, taxonomy tables, and ASV fasta files ...
  • (16s) No 3. Diversity (16s rRNA) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Output files from the No 3. Diversity Workflow page of the Bocas Hypoxia study.File names and descriptions:<B>16s-water.rdata: </B>contains all variables and phyloseq objects from the pipeline. To see the <B>Objects</B>, ...
  • (16s) No 4. Differentially Abundant ASVs (16s rRNA) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Output files from the No 4. Differentially Abundant ASVs page of the Bocas Hypoxia study.File names and descriptions:<B>da_asvs_pipeline.rdata</B>: contains all variables and objects from the pipeline. To see the Objects, ...
  • Asteroid 16S alignment 
    Collin, Rachel; Venera-Pontón, Dagoberto E. (The Smithsonian Institution, 2020)
    These are the 16S data used for ABGD analysis mentioned in the methods of the 2020 paper in Invertebrate Biology: <B>How I wonder what you are: Can DNA barcoding identify the larval asteroids of Panama?</B>
  • Asteroid COI data 
    Collin, Rachel; Venera-Pontón, Dagoberto E. (The Smithsonian Institution, 2020)
    This is the fasta file of the COI sequences used to generate Figure 1 and used the the 2020 Invertebrate Biology paper: <B>How I wonder what you are: Can DNA barcoding identify the larval asteroids of Panama?</B>
  • Data supporting Invertebrate Biology: Knots, spoons, and cloches: DNA barcoding unusual larval forms helps document the Diversity of Neotropical Marine Annelids 
    Collin, Rachel; Venera-Pontón, Dagoberto E. (The Smithsonian Institution, 2020)
    This includes the datasets and scripts prepared by Dagoberto Venera-Ponton from our paper: <B>Knots, spoons, and cloches: DNA barcoding unusual larval forms helps document the Diversity of Neotropical Marine Annelids.</B>
  • Dataset: Context-dependent carryover effects of hypoxia and warming in a coastal ecosystem engineer 
    Donelan, Sarah C.; Ogburn, Matthew B.; Breitburg, Denise L. (The Smithsonian Institution, 2020)
    Experimental design and methods described in Donelan et al., Ecological Applications
  • Freeman et al., 2020 ISME J isotope data.xlsx 
    Freeman, Christopher; Paul, Valerie J. (The Smithsonian Institution, 2020)
    Stable isotope, photosymbiont abundance (chlorophyll a values), and elemental values (%C, %N, and C:N) for diverse and common Caribbean sponges (Porifera) from the Florida Keys, Belize, Honduras, and Bocas del Toro, ...
  • Luidia 16S alignment 
    Collin, Rachel; Venera-Pontón, Dagoberto E. (The Smithsonian Institution, 2020)
    This is the fasta file of the Luidia 16S alignment from the 2020 paper in Invertebrate Biology entitled <B>How I wonder what you are: Can DNA barcoding identify the larval asteroids of Panama?</B>
  • (mg) No 3. Assembly &amp; Annotations (metagenomes) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    The complete output of the Snakemake workflow describe in the reference linked below. Zipped directories contain the outputs of each step from the workflow. Please note that some information contained in the contigs.db and ...
  • (mg) No 4. Assembly &amp; Annotation Summary (metagenomes) output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Krona plots for Kraken short-read taxonomy and Kaiju contig taxonomy. File names and descriptions as follows:<B>cc-kraken.html</B>: Short-read Kraken Krona plots for site Coral Caye (cc).<B>cr-kraken.html</B>: Short-read ...
  • (mg) No 5. Binning MAGs (metagenomes) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Binning summary data for four collections: 1) <B>CONCOCT_5</B>, the automatic binning, 2) <B>VIRAL_FINAL</B>, the bins after manual refinement deemed to be viral, 3) <B>MICROBIAL_FINAL</B>, the bins after manual refinement ...
  • (mg) No 6. MAG02 Phylogenomic Analysis (metagenome) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Files generated from the pangenomic (<B>01_MAG02_PAN</B>/), phylogenomic (<B>02_MAG02_PHYLOGENOMICS</B>), and 16S rRNA phylogenetic (<B>03_MAG02_16S_rRNA_PHYLOGENETICS</B>) analyses of MAG02. You can use the anvi&#39;o ...
  • No. 0: Raw 16S rRNA fastq data files for Bocas hypoxia study 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    This repository contains the RAW sequencing data for hypoxia study. Trimmed reads (with primers removed) are deposited at the European Nucleotide Archive, study accession number PRJEB36632 (ERP119845).Raw fastq data files ...

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