Data from: A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences

Schwartz TS, Tae H, Yang Y, Mockaitis K, Van Hemert JL, Proulx SR, Choi J, Bronikowski AM

Date Published: May 26, 2015

DOI: http://dx.doi.org/10.5061/dryad.tg58v

 

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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 GarterSnakeTranscriptome.ContigsOnly
Downloaded 3 times
Description This is the multi-organ garter snake transcriptome assembled from 454 data. This file contains only the contigs.
Download 454AllContigs.fna (51.71 Mb)
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Title GarterSnakeTranscriptome.Contigs.and.Singletons
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Description This garter snake transcriptome contains all the contigs and singletons. Sequence IDs in this file corresponds to the SeqID column in the Annotation File
Download 454Contigs_Newb_Mira_sing.fna (100.5 Mb)
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Title Annotation File
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Description This is the Annotation file that corresponds to the transcriptome contigs and singletons
Download AnnoData_updated2010.08.16.xlsx (31.56 Mb)
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Title Add.file1_Table_Samples
Downloaded 3 times
Description Additional files that are also available from BMC Genomics website. Additional file 1 – Table containing details of the samples used for the sex-specific RNA pools. Tissue samples of the same type were pooled across individuals (either laboratory or field born animals) for total RNA extraction. Extracted pools of RNA were quantified and the quality checked on the Bioanalyzer. Equal amounts of RNA from each tissue type were pooled by sex.
Download Add.file1_Table_Samples.doc (47.61 Kb)
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Title Add.file2_Dist.Reads
Downloaded 12 times
Description Additional files that are also available from BMC Genomics website. Additional file 2 – Graphs illustrating the size distribution of the reads for each sex. Length (bp) distribution of reads obtained with the 454 GS-FLX Titanium sequencing. Read number (N) and length (L) in base pairs. A) Female run. B) Male runs.
Download Add.file2_Dist.Reads.pdf (30.76 Kb)
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Title Add.file3_Graph-cluster.description
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Description Additional files that are also available from BMC Genomics website. Additional file 3 – Description of NEWBLER assembly and graph-clustering procedure.
Download Add.file3_Graph-cluster.description.pdf (145.4 Kb)
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Title Add.file4_GOgraphs
Downloaded 10 times
Description Additional files that are also available from BMC Genomics website. Additional file 4 – Pie graphs of GO assignments. GO slim (level 1, Biological Processes) assignments for all the sequences with annotation, broken down by class of sequences: male singletons, male contigs, both contigs (containing male and female reads), female contigs, female singletons.
Download Add.file4_GOgraphs.pdf (18.90 Kb)
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Title Add.file5_mapAnoCar1
Downloaded 122 times
Description Additional files that are also available from BMC Genomics website. Additional file 5 - Snake transcripts mapped to coding and non-coding regions of the Anolis lizard draft genome (AnoCar1.0). A 2007 Excel file (.xlsx) providing details where the snake transcripts mapped to the Anolis draft genome. See the ReadME tab for description of columns.
Download Add.file5_mapAnoCar1.xls (10.01 Mb)
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Title Add.file6_Clustering
Downloaded 18 times
Description Additional files that are also available from BMC Genomics website. Additional file 6 - Clustering based on homology and contig-graphs. A) Distribution of the number of contigs in a HomoloGene accession, and B) the number of HomoloGene accessions that a contig is assigned to, both at e-value =1e-20. C) Distribution of the number of contigs belonging to a graph-cluster.
Download Add.file6_Clustering.pdf (14.60 Kb)
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Title Add.file7_Variants
Downloaded 3 times
Description Additional files that are also available from BMC Genomics website. Additional file 7 – Details of variants. A 2007 Excel file (.xlsx) providing details for the variants (SNPs and INDELs). See the ReadME tab for description of columns.
Download Add.file7_Variants.xlsx (8.385 Mb)
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Title Add.file8_ContigOfInterest
Downloaded 2 times
Description Additional files that are also available from BMC Genomics website. Additional file 8 - Contigs of interest. A 2007 Excel file (.xlsx) containing the sequences of interest including those that are sex-specific, that have homology to the chicken Z chromosome, those in the 1st percentile of TS/TV ratios, those in the top 99th percentile of Ka/Ks ratios, and those in the top 99th percentile of variability (number of variants per bp). See the ReadME tab for description of columns.
Download Add.file8_ContigOfInterest.xlsx (201.0 Kb)
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Title Add.file9_sex-specificGOgraph
Downloaded 19 times
Description Additional files that are also available from BMC Genomics website. Additional file 9 – Sex-specific enrichment of GO terms (level 2, Biological Processes) assigned to the 190 sex-specific sequences. The * indicates the significant over-enrichment of sequences involved in biosynthetic processes in the female-specific sequences (Fisher’s Exact Test, FDR <0.006, p-value < 0.0002).
Download Add.file9_sex-specificGOgraph.pdf (17.23 Kb)
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When using this data, please cite the original publication:

Schwartz TS, Tae H, Yang Y, Mockaitis K, Van Hemert JL, Proulx SR, Choi J, Bronikowski AM (2010) A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences. BMC Genomics 11: 694. http://dx.doi.org/10.1186/1471-2164-11-694

Additionally, please cite the Dryad data package:

Schwartz TS, Tae H, Yang Y, Mockaitis K, Van Hemert JL, Proulx SR, Choi J, Bronikowski AM (2010) Data from: A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.tg58v
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