This repository contains all of the code necessary to generate the analyses presented in this paper, including the manuscript itself.
- data -- basic analyses and combining of aligned/called sequences
- fastq -- fastq files and makefiles to assemble, align, call, and annotate all of the sequences in all of the species examined
- manuscript -- R and LaTeX code to produce the published manuscript
- figures -- various complicated figures which are produced separately from the manuscript
- alignments -- alignments of genomic regions of interest in species studied with known genomes
- promoters -- promoter peak data for placenta samples in humans
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all_species_mean_fpkm.txt.xz contains all of the mean FPKM for each species. This was supposed to be included in the supplemental material of the paper, but was missing for some reason.
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all_species_per_sample_fpkm.txt.xz contains the FPKM per sample across all samples in each species. This file was also missing from supplemental material for some reason.
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placenta_core_transcriptome.txt.xz contains the FPKM of all genes in the core placenta transcriptome in long format. [One row per gene in each species, including the "all but one", "all", "all but metatherian" minimum FPKM in the set of species as depicted in the graphs included in the paper.]
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placenta_classification_shape_p_fdr.txt.xz contains the p, fdr, and overall fdr values of the glm of the association of gene expression with placenta shape, interdigitation, and intimacy which are shown in supplemental figures 57,58, and 60. [I have excluded the ordered analysis for clarity.]