Data from: Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations

Harris SE, O'Neill RJ, Munshi-South J

Date Published: July 1, 2014

DOI: http://dx.doi.org/10.5061/dryad.6hc0f

 

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Title Table S1. SSR sequences and primers (doc file)
Downloaded 38 times
Description Table of microsatellite repeats identified using MsatCommander and sorted by motif. Only repeats with suitable flanking sequence for primer design were kept. Primer sequences designed using Primer3 are also listed.
Download Table_S1_Peromyscus_SSR.docx (89.41 Kb)
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Title Table S2. Chromosomal order and assignment (csv file)
Downloaded 31 times
Description Comma-delimited spreadsheet listing contig names that were assigned to Peromyscus chromosomes. Contigs are sorted by start of alignment in the chromosome and are displayed in typical BLAST –m6 (tabular) format.
Download TableS2_Peromyscus_Linkage_Map.xlsx (1.805 Mb)
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Title Contig sequences for P. leucopus transcriptome (fasta file)
Downloaded 17 times
Description Transcriptome contigs assembled from raw SOLiD 5500 xl sequencing reads using Trinity. Only contigs with high-quality open reading frames identified from Transdecoder and unique contigs with best match hits to Mus musculus Uniprot protein database using BLASTN were kept.
Download Pleucopus_Transcriptome_Contigs.fasta (30.52 Mb)
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Title Information on SNPs identified from transcriptome data (vcf file)
Downloaded 8 times
Description SNPs identified from transcriptome alignment files in variant call format. SNPs were identified using GATK. Parameters and filters for calling SNPs are listed in header. Additional hard filters include removal of SNPs where every individual was heterozygous, overall SNP depth > 10, overall SNP depth < 350, and minor allele frequency (MAF) > 0.025.
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Title Annotation information, BLAST results, Gene Ontology (.dat file for Blast2GO)
Downloaded 10 times
Description Standard input file for BLAST2GO. This file can be loaded directly into .jnlp executable file downloaded from BLAST2GO website. Includes BLASTX results against NCBI’s non-redundant protein database and Gene Ontology information based on best hit gene matches.
Download Pleucopus_Transcriptome_blast2go.dat (31.79 Mb)
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Title R scripts, bash scripts, and full analysis workflow (txt file)
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Description This text file represents the working lab notebook of all software, scripts, and command line usage dating from when the raw data were received to when the final figures and tables were produced.
Download LabNotebook_Scripts.txt (255.5 Kb)
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Title Contig sequences for P. leucopus transcriptome (fasta file)
Downloaded 7 times
Description A second transcriptome is included named, “Pleucopus_Transcriptome_Contigs_Annotated.fasta”. This file includes unique contigs that mapped to the Mus musculus transcriptome. Gene annotations are included in the header for each sequence.
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Title Alternative splice events identified in Peromyscus leucopus transcriptome
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Description This FASTA file contains two sequences for each alternative splicing sequence, labeled as upper and lower splice, that was identified in the Peromyscus leucopus transcriptome.
Download Pleucopus_Transcriptome_AlternativeSplice_...fasta (124.4 Kb)
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Title Contigs from Peromyscus leucopus transcriptome that represent splice variants
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Download Pleucopus_Transcriptome_AlternativeSplice_...fasta (2.053 Mb)
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When using this data, please cite the original publication:

Harris SE, O'Neill RJ, Munshi-South J (2015) Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations. Molecular Ecology Resources 15(2): 382-394. http://dx.doi.org/10.1111/1755-0998.12301

Additionally, please cite the Dryad data package:

Harris SE, O'Neill RJ, Munshi-South J (2014) Data from: Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6hc0f
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