Data from: Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents

Marra NJ, DeWoody JA

Date Published: December 3, 2014

DOI: http://dx.doi.org/10.5061/dryad.qn474

 

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Title Dipodomys spectabilis spleen transcriptome
Downloaded 24 times
Description Combined assembly of 454 reads and fragmented Illumina assembly (see methods of associated paper) in gsAssembler version 2.6.
Download D_spec_spleen_filtered.fasta (57.01 Mb)
Download README.txt (1.188 Kb)
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Title Chaetodipus baileyi spleen transcriptome
Downloaded 9 times
Description Transcriptome assembly from combined assembly Illumina reads. These reads were assembled first in Trinity and then fragmented and assembled in gsAssembler (see methods of manuscript for more details and rationale)
Download C_bail_spleen_filtered.fasta (45.80 Mb)
Download README.txt (1.179 Kb)
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Title Heteromys desmarestianus spleen transcriptome
Downloaded 21 times
Description Combined assembly of 454 reads and fragmented Illumina assembly (see methods of associated paper) in gsAssembler version 2.6.
Download README.txt (1.191 Kb)
Download H_desm_spleen_filtered.fasta (44.15 Mb)
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Title D_spec_spleen_top_blast_data
Downloaded 28 times
Description These are the preliminary blast descriptions for contigs from the combined assembly of Illumina reads and 454 reads pooled from 4 individual Dipodomys spectabilis spleen libraries. Descriptions are from a BLASTx search of the Swiss-Prot database at e<1x10^-6. The combined assembly was conducted in gsAssembler version 2.6 and contigs that were smaller than 100 bp have been removed. This accounts for the gaps in contig names (e.g. if contig 2 from the gsAssembler asembly was smaller than 100 bp and removed prior to blast annotation then the first two contigs are contig 1 and contig 3).
Download D_spec_spleen_top_blast_data.txt (4.666 Mb)
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Title Heteromys_desmarestianus_spleen_top_blast_data
Downloaded 208 times
Description These are the preliminary blast descriptions for contigs from the combined assembly of Illumina reads and 454 reads pooled from 4 individual Heteromys desmarestianus spleen libraries. Descriptions are from a BLASTx search of the Swiss-Prot database at e<1x10^-6. The combined assembly was conducted in gsAssembler version 2.6 and contigs that were smaller than 100 bp have been removed. This accounts for the gaps in contig names (e.g. if contig 2 from the gsAssembler asembly was smaller than 100 bp and removed prior to blast annotation then the first two contigs are contig 1 and contig 3).
Download H_desm_spleen_top_blast_data.txt (3.487 Mb)
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Title Chaetodipus_baileyi_spleen_top_blast_data
Downloaded 29 times
Description These are the preliminary blast descriptions for contigs from the combined assembly of Illumina reads pooled from 4 individual Chaetodipus baileyi spleen libraries. Descriptions are from a BLASTx search of the Swiss-Prot database at e<1x10^-6. The combined assembly was conducted in gsAssembler version 2.6 and contigs that were smaller than 100 bp have been removed. This accounts for the gaps in contig names (e.g. contig 2 from the gsAssembler asembly was 25 bp long and removed prior to blast annotation so the first two contigs are contig 1 and contig 3).
Download C_bail_spleen_top_blast_data.txt (3.399 Mb)
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Title COI_Guide_TREE_Marked_H_desm
Downloaded 11 times
Description This is the tree that was used in codeml as a guide tree for the branch and branch-site tests (see text of methods). The tree is unrooted to as is required for these tests. The tropical lineage, Heteromys desmarestianus has been marked with #1 to indicate it as the foreground branches to be assigned a different rate than the rest of the tree. D_spec = Dipodomys spectabilis, C_bail = Chaetodipus baileyi, H_desm = Heteromys desmarestianus, M_musc = Mus musculus.
Download COI_Guide_TREE_Marked_H_desm.txt (35 bytes)
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Title perl_script_for_alignments
Downloaded 17 times
Description This is the perl script that was used to produce the multiple sequence alignments necessary for the paper associated with this data package. The script has been uploaded as was used for the analysis and therefore would need to be adapted slightly for custom analyses (this script is designed to take four fasta files and then conduct an msa on a set of 4 sequences, one from each of the four files in order. This could be adjusted to accomodate additional or fewer taxa. The script is commented and questions should be directed to Nicholas Marra regarding it. To replicate the analysis conducted for this paper, the inputs to the script should be four files from a reciprocal best blast analysis that have been trimmed to the start and stop codons of a full cds region. Alignments from the script were further analyzed in codeml of PAML 4.7 to assess selection and alignments that were significant were then visually inspected. See paper for details, note in the paper the 4th taxa was Mus musculus and was necessary for obtaining cds information.
Download perl_script_for_alignments.pl (15.20 Kb)
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Title Spleen_R_commands_dryad
Downloaded 8 times
Description This file contains the R commands that were used to run DESeq for the differential expression analysis described in this paper. The program DESeq was introduced in the following paper: Simon Anders and Wolfgang Huber. Differential expression analysis for sequence count data. Genome Biology, 11:R106, 2010. The commands and information about the function of these commands largely derive from the manual and documentation of this program written by Simon Anders that is available through the bioconductor page for DESeq.
Download Spleen_R_commands_dryad.txt (3.63 Kb)
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When using this data, please cite the original publication:

Marra NJ, DeWoody JA (2014) Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents. BMC Genomics 15: 929. http://dx.doi.org/10.1186/1471-2164-15-929

Additionally, please cite the Dryad data package:

Marra NJ, DeWoody JA (2014) Data from: Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.qn474
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