Data from: Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement and pancrustacean phylogeny

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Conchoecissa sequence data
Downloaded 34 times
Description Assembled 454 transcriptome data, otherwise unpublished. Only sequences used in MBE-published phylogenetic analysis are provided here. Collection information: Trawl Lower Sur Canyon on R/V Western Flyer Trawl on Western Flyer 36.06° N 122.29 W December 10th, 2009
Download Conchoecissa_sp.fasta (79.36 Kb)
Details View File Details
Title Morphological matrix for phylogenetics
Description Morhpological data matrix, including extant and fossil taxa. Stored in Morphobank, project ID 689 <http://dx.doi.org/10.7934/P689>
Download //dx.doi.org/10.7934/P689 (0 bytes)
Details View File Details
Title Raw 454: Vestalenula_sp
Downloaded 31 times
Description Raw Transcriptome sequence from full bodies. Adapter sequences included. Pooled together multiple individuals. Adapter = AAGCAGTGGTATCAACGCAGAGTACTTTTTTCTTTTTT. Collection Information: Freshwater Puddle, Isla Colon, Bocas del Toro, Panama. Net collecting 9º21.17'N 82º15.45'W July 29th, 2009 10cm
Download Vestalenula_sp.fasta (12.02 Mb)
Details View File Details
Title Raw 454: Vestalenula_sp quality file
Downloaded 23 times
Description Quality associated with fasta file.
Download Vestalenula_sp.fasta.qual (35.08 Mb)
Details View File Details
Title Raw 454: Euphilomedes_morini_Compound_Eyes
Downloaded 19 times
Description Euphilomedes morini. 454 transcriptome data. from compound eyes. Pooled ~50 animals together (100 eyes). Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Stern’s Wharf Pier, Santa Barbara, CA Eckman grab 34º24.4'N 119º40.5'W Oct., Nov., 2008 10 m depth.
Download Euphilomedes_morini_Compound_Eyes.fasta (12.77 Mb)
Details View File Details
Title Raw 454: Euphilomedes_morini_Compound_Eyes.fasta
Downloaded 26 times
Description Quality file associated with fasta sequence file
Download Euphilomedes_morini_Compound_Eyes.fasta.qual (37.08 Mb)
Details View File Details
Title Raw 454: Euphilomedes_morini median eye transcriptome
Downloaded 33 times
Description Euphilomedes morini. 454 transcriptome data from median eyes. Pooled ~50 animals together (50 eyes). Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Stern’s Wharf Pier, Santa Barbara, CA Eckman grab 34º24.4'N 119º40.5'W Oct., Nov., 2008 10 m depth.
Download Euphilomedes_morini_Median_Eyes.fasta (21.27 Mb)
Details View File Details
Title Raw 454: Euphilomedes_morini_Median_Eyes quality
Downloaded 13 times
Description Quality file associated with fasta sequence file
Download Euphilomedes_morini_Median_Eyes.fasta.qual (61.90 Mb)
Details View File Details
Title Raw 454: Cytherelloidea_californica
Downloaded 23 times
Description Cytherelloidea californica. 454 transcriptome data. from full bodies. Pooled 26 animals together (50 eyes). Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Camino de la Costa Beach Access, La Jolla, San Diego algae collecting 24º46.9'N 80º54.58'W May 14th, 2010 intertidal only on very low tide
Download Cytherelloidea_californica.fasta (82.81 Mb)
Details View File Details
Title Raw 454: Cytherelloidea_californica quality file
Downloaded 37 times
Description Quality file associated with fasta sequence file
Download Cytherelloidea_californica.fasta.qual (241.6 Mb)
Details View File Details
Title Raw 454: Puriana_sp_Bodies
Downloaded 21 times
Description Puriana sp. 454 transcriptome data. from Bodies minus median eyes. Pooled multiple animals together. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Isla Colon, Bocas del Toro, Panama net collecting 9º21'N 82º15.45'W July 23rd, 2009 1m depth
Download Puriana_sp_Bodies.fasta (12.61 Mb)
Details View File Details
Title Raw 454: Puriana_sp_Median_Eyes quality file
Downloaded 26 times
Description Quality file associated with fasta sequence file
Download Puriana_sp_Median_Eyes.fasta.qual (106.7 Mb)
Details View File Details
Title Raw 454: Puriana_sp_Median_Eyes
Downloaded 36 times
Description Puriana sp. 454 transcriptome data. from Median Eyes. Pooled multiple animals together. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Isla Colon, Bocas del Toro, Panama net collecting 9º21'N 82º15.45'W July 23rd, 2009 1m depth
Download Puriana_sp_Median_Eyes.fasta (36.54 Mb)
Details View File Details
Title Raw 454: Puriana_sp_Bodies quality file
Downloaded 20 times
Description Quality file associated with fasta sequence file
Download Puriana_sp_Bodies.fasta.qual (36.81 Mb)
Details View File Details
Title Raw 454: Heterocypris_sp_Bodies
Downloaded 19 times
Description Heterocypris sp. 454 transcriptome data. bodies minus eyes. Pooled 30 animals together. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Temporary Freshwater Pool, More Mesa, Santa Barbara, CA net collecting 34º25.23'N 119º47.29'W 10cm depth
Download Heterocypris_sp_Bodies.fasta (39.67 Mb)
Details View File Details
Title Raw 454: Heterocypris_sp_Bodies Quality file
Downloaded 21 times
Description Quality file associated with fasta sequence file
Download Heterocypris_sp_Bodies.fasta.qual (115.6 Mb)
Details View File Details
Title Raw 454: Heterocypris_sp_Median_Eyes
Downloaded 37 times
Description Heterocypris sp. 454 transcriptome data median eyes. Pooled 100 eyes together Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Temporary Freshwater Pool, More Mesa, Santa Barbara, CA net collecting 34º25.23'N 119º47.29'W 10cm depth
Download Heterocypris_sp_Median_Eyes.fasta (36.17 Mb)
Details View File Details
Title Raw 454: Heterocypris_sp_Median_Eyes quality file
Downloaded 20 times
Description Quality file associated with fasta sequence file
Download Heterocypris_sp_Median_Eyes.fasta.qual (105.1 Mb)
Details View File Details
Title Raw 454: Skogsbergia_lerneri_Compound_Eyes
Downloaded 39 times
Description Skogsbergia lerneri. 454 transcriptome data. compound eyes (more than 50 pooled together). Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Duck Key Viaduct, FL. bait trap. 24º46.9'N 80º54.58'W. July 16th thru July 18th, 2009. 2-3m depth.
Download Skogsbergia_lerneri_Compound_Eyes.fasta (42.06 Mb)
Details View File Details
Title Raw 454: Skogsbergia_lerneri_Compound_Eyes quality file
Downloaded 28 times
Download Skogsbergia_lerneri_Compound_Eyes.fasta.qual (122.8 Mb)
Details View File Details
Title Raw 454: Skogsbergia_lerneri_Median_Eyes
Downloaded 34 times
Description Skogsbergia lerneri. 454 transcriptome data. median eyes (more than 50 pooled together). Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Duck Key Viaduct, FL. bait trap. 24º46.9'N 80º54.58'W. July 16th thru July 18th, 2009. 2-3m depth.
Download Skogsbergia_lerneri_Median_Eyes.fasta (44.33 Mb)
Details View File Details
Title Raw 454: Skogsbergia_lerneri_Median_Eyes quality file
Downloaded 17 times
Description Quality file associated with fasta sequence file
Download Skogsbergia_lerneri_Median_Eyes.fasta.qual (129.5 Mb)
Details View File Details
Title Raw 454: Vargula_tsujii_Body1
Downloaded 36 times
Description Vargula tsujii. 454 transcriptome data. 33 Bodies minus eyes. Two separate runs of 454 from same RNA. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Fishermen’s Cove, Twin Harbors, Catalina Island, CA bait trap 33º26.66'N 118º29.34'W July 10th and 11th, 2009 Depth: 5-10m
Download Vargula_tsujii_Body1.fasta (25.45 Mb)
Details View File Details
Title Raw 454: Vargula_tsujii_Body1 quality file
Downloaded 21 times
Description Quality file associated with fasta sequence file
Download Vargula_tsujii_Body1.fasta.qual (74.34 Mb)
Details View File Details
Title Raw 454: Vargula_tsujii_Body2
Downloaded 26 times
Description Vargula tsujii 454 transcriptome data. 33 Bodies minus eyes. Two separate runs of 454 from same RNA. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Fishermen’s Cove, Twin Harbors, Catalina Island, CA bait trap 33º26.66'N 118º29.34'W July 10th and 11th, 2009 Depth: 5-10m
Download Vargula_tsujii_Body2.fasta (36.62 Mb)
Details View File Details
Title Raw 454: Vargula_tsujii_Body2.fasta
Downloaded 24 times
Description Quality file associated with fasta sequence file
Download Vargula_tsujii_Body2.fasta.qual (106.8 Mb)
Details View File Details
Title Raw 454: Actinoseta_jonesi
Downloaded 24 times
Description Actinoseta jonesi 454 transcriptome data. Full bodies including eyes. Multiple pooled individuals. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Cayo Enrique, La Parguera, Puerto Rico net collecting 17°57.335’N 67°03.185’W September 12th, 2010 2-3m depth.
Download Actinoseta_jonesi.fasta (75.04 Mb)
Details View File Details
Title Raw 454: Actinoseta_jonesi quality files
Downloaded 18 times
Description Quality file associated with fasta sequence file
Download Actinoseta_jonesi.fasta.qual (218.9 Mb)
Details View File Details
Title Data used in phylogenetic analyses
Downloaded 62 times
Description Data used in phylogenetic analyses, in column separated text format. First column is species name, second column is name of data partition, third column is a unique id for the species/partition data (ie GenBank GI number), fourth column is sequence or morphological data. The sequence data are derived from the raw 454 data, or from other sources. Raw 454 data was assembled using Newbler. We pulled genes from transcriptomes using Hamstr. We then aligned sequences with MUSCLE, and cut out ambiguously aligned regions with AliScore/AliCut. Unique identifiers with "Voucher" in the name are previously unpublished, and will be placed in GenBank. This 4-column data format can be used with many tools developed in the Osiris package for conducting phylogenetics in Galaxy.
Download FullData.csv (3.961 Mb)
Details View File Details

When using this data, please cite the original publication:

Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK (2012) Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement and pancrustacean phylogeny. Molecular Biology and Evolution 30(1): 215-233. http://dx.doi.org/10.1093/molbev/mss216

Additionally, please cite the Dryad data package:

Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK (2012) Data from: Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement and pancrustacean phylogeny. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.tb40v
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: