Data from: Transcriptomics of colour patterning and colouration shifts in crows

Poelstra JW, Vijay N, Höppner MP, Wolf JBW

Date Published: August 27, 2015

DOI: http://dx.doi.org/10.5061/dryad.hv333

 

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Title Hooded crow genome annotation v2.7A
Downloaded 9 times
Description Whole-genome annotation file for hooded crow (Corvus [corone] cornix) in gff format.
Download C.c.cornix_annotation_v2.7A.gff (1.110 Gb)
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Title RSEM output (gene counts)
Downloaded 9 times
Description Contains the gene counts for each library as produced by the RSEM software. For each tissue, a separate file is provided, in which columns are libraries (with the library identifiers corresponding to those in the file containing metadata by library) and rows are genes (with gene identifiers as in the annotation file).
Download RSEM.output.tar.gz (3.569 Mb)
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Title PCA input
Downloaded 16 times
Description A matrix with the input data (normalized gene counts) for the PCA that is presented in the paper. Columns are libraries (with the library identifiers corresponding to those in the file containing metadata by library) and rows are genes (with gene identifiers as in the annotation file).
Download PCA.input.txt (6.342 Mb)
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Title Differential expression results (edgeR and ebseq output)
Downloaded 11 times
Description Contains files with results of the differential expression analyses conducted with edgeR and Ebseq. Separate files are present for each program for each of the comparisons that were made. Comparisons were made between carrion and hooded crow for each of the tissues: forebrain, liver, gonads, skin_bodypool (skin from torso), and skin_headpool (skin from head), and between body regions for each of the taxa: skin_CC (carrion crow skin) and skin_CX (hooded crow skin). For example, the file "ebseq_liver.txt" presents the results of carrion vs. hooded crow in liver performed with Ebseq. In each file, the columns are: gene_id (gene identifiers as in the annotation file), FDR (False Discovery Rate) and LFC (Log-Fold Change).
Download edgeR.and.ebseq.output.tar.gz (2.602 Mb)
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Title Metadata by individual
Downloaded 5 times
Description Metadata for each crow sampled in this study: including population of origin, GPS coordinates, dates of feather plucking, dates of sampling, times of day of sampling, weight at sampling, approximate age at sampling, and number of days of feather regrowth until sampling.
Download metadata_individuals.txt (1.718 Kb)
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Title Metadata by library
Downloaded 12 times
Description Metadata for each RNA-seq library used in this study, including the tissue and individual (see the metadata by individual file for more info on each individual) from which the library is derived, and the SRA accession numbers. Columns: "library_ID" (library identifier 2), "library_code" (library identifier 2), "individual_short" (individual ID, same as in metadata by individual file), "tissue_long" (name of tissue), "use_for_DE" (whether the sample was used for differential expression analysis (if TRUE) or only for annotation improvement (if FALSE), "Biosample_ID" (SRA Biosample identifier), "SRR_ID" (SRA run ID), "SRS_ID" (SRA sample ID), "sample".
Download metadata_libraries.txt (12.59 Kb)
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Title tophat and cufflinks script
Downloaded 8 times
Description This script will download our RNA-seq data from SRA (using the SRR IDs that can be found in metadata by library), use Tophat to map it to the genome (genome fasta file should be in the working dir), and then run Cufflinks.
Download tophat_script.sh (2.378 Kb)
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When using this data, please cite the original publication:

Poelstra JW, Vijay N, Höppner MP, Wolf JBW (2015) Transcriptomics of colour patterning and colouration shifts in crows. Molecular Ecology 24(18): 4617–4628. http://dx.doi.org/10.1111/mec.13353

Additionally, please cite the Dryad data package:

Poelstra JW, Vijay N, Höppner MP, Wolf JBW (2015) Data from: Transcriptomics of colour patterning and colouration shifts in crows. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hv333
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