Data from: Tracing the dynamics of gene transcripts after organismal death

In life, genetic and epigenetic networks precisely coordinate the expression of genes—but in death, it is not known if gene expression diminishes gradually or abruptly stops or if specific genes and pathways are involved. We studied this by identifying mRNA transcripts that apparently increase in relative abundance after death, assessing their functions, and comparing their abundance profiles through postmortem time in two species, mouse and zebrafish. We found mRNA transcript profiles of 1063 genes became significantly more abundant after death of healthy adult animals in a time series spanning up to 96 h postmortem. Ordination plots revealed non-random patterns in the profiles by time. While most of these transcript levels increased within 0.5 h postmortem, some increased only at 24 and 48 h postmortem. Functional characterization of the most abundant transcripts revealed the following categories: stress, immunity, inflammation, apoptosis, transport, development, epigenetic regulation and cancer. The data suggest a step-wise shutdown occurs in organismal death that is manifested by the apparent increase of certain transcripts with various abundance maxima and durations.MiceProbesParameters1. Columns: ProbeID, a, b, R2, CurveType. The CurveType refers to whether the best curve was Langmuir (LG) or Freundlich (F). The empirical parameters a and b in the Freundlich equation refer to the pre-exponent and the exponent (Y=a*Xb) respectively. The empirical parameters a and b in the Langmuir equation Y=Ymax*K*X/(1+K*X), where a = 1/(K*Ymax); b = 1/Ymax. The R2 refers to the fit of the empirical data to curve.FishProbesParameters1. Columns: ProbeID, a, b, R2, CurveType. The CurveType refers to whether the best curve was Langmuir (LG) or Freundlich (F). The empirical parameters a and b in the Freundlich equation refer to the pre-exponent and the exponent (Y=a*Xb) respectively. The empirical parameters a and b in the Langmuir equation Y=Ymax*K*X/(1+K*X), where a = 1/(K*Ymax); b = 1/Ymax. The R2 refers to the fit of the empirical data to curve.Mouse_liver_Log10_AllProfilesColumns: ProbeID, gene transcript abundances at postmortem stages 1 to 7.Mouse_brain_Log10_AllProfiles.txtColumns: ProbeID, gene transcript abundances at postmortem stages 1 to 7.Fish_Log10_AllProfilesColumns: ProbeID, gene transcript abundances at postmortem stages 1 to 10.MiceProbesSeqColumns: ProbeID, gene transcript abundances at postmortem stages 1 to 10.FishProbesSeqProbeIDs and DNA sequences.Gene_annotation_lit_refsMS Excel spreadsheet of zebrafish and mouse probe/gene annotations and functional categorizations: File_GenesLitRefs. Columns: microarray probe names, phylostrata, NCBI gene names, cluster, regulator, response, functional categorization fields 1 to 4, formal gene name, References