mingwhy / cell.dynamics_aging.asynchrony

cell.dynamics_aging.asynchrony

This foder contains source code for data analysis in manuscript "Cellular age drives asynchronous transcriptome aging" by Ming Yang, Benjamin R. Harrison, Daniel E.L. Promislow.

cell_demography_model

This folder contains code scripts for Figure 1B, Supplemental Fig. S1, and S2, based on the cell demography model we developed to model cell population dynamics in Supplemental Methods and cell lifespan data in mice in Supplemental Table S1.

TMS_transcriptome_variation

• 00_setup_mouseID.R, select cell types from TMS with avaible mouse cell lifespan estimates in Sender and Milo (2021)
• 01_countland_subsample.transcripts.R, down-sampling cells to have an equal number of trancripts per tissue:cell type combination.
• 02.1_find_invariant_gene_per.mouse.R, identity genes whose expression level didn't change significant with organismal age. A detailed pipeline is shown in Supplemental Fig. S4.
• 02.2_invar.gene_lmer_beta_age_per.mouse.R, use age-invariant genes to compute gene expression variability per age group per mouse individual, Supplemental Fig. S5
• 03.1_change.in.expr_change.in.cell.age.R, quantify the age effect on gene expression variability measured by coefficient variation (CV), plot the relationship between beta_age and change in mean cell age as shown in Figure 2B.
• 03.2_change.in.expr_change.in.cell.age_endothelia.cells.only.R, exmamine tissue microenvironment effect in endothelial cells, Supplemental Fig. S10.
• 04_run_dist_spearman.cor-1_per.mouse.R, effect of age on transcriptome variability measued by cell-cell correltaions, Supplemental Fig. S6.
• 04_run_GCL_decibel_gcl_per.mouse.R, effect of age on transcriptome variability measued by GCL, Supplemental Fig. S7.
• 04.1_alternative.metric_log2ratio_change.in.cell.age_per.mouse.R, integrate effect of age on transcriptome variability via different metrics, Supplemental Table S2.
• 05_mean.cell.age_obs.CV_per.mouse.R, 05_mean.cell.age_obs.gcl_per.mouse.R, and 05_mean.cell.age_obs.spearman.cor_per.mouse.R, plot the relationship between cellular age and transcriptome variability as shown in Figure 2A and Supplemental Fig. S8.
• 05_mean.cell.age_obs.CV_per.mouse_female.R, plot the relationship between cellular age and transcriptome variability in female mice as shown in Supplemental Fig. S9.

GO_term_expression

GO term expression analysis for Figure 3 and Supplemental Fig. S11.

dNdS_analysis

• mouse_rat, , dN/dS analysis with mouse-rat orthologous genes, Figure 4, Supplemental Fig. S12 and S13.
• mouse_human, dN/dS analysis with mouse-human orthologous genes, Supplemental Fig. S14.

src

• src_barplot_lifespan_byTissue.R, plot the distribution of cell lifespan data used in our study as shown in Figure 1A.
• src_compare_facs_droplet_depth.R, TMS dataset overview in Supplemental Fig. S3
• src_TMS_genes_id.mapping.R, TMS data gene id mapping.
• src_cell.demography_cell.age.difference.R, generate cell age difference between organismal ages.
• src_mouse_rat_biomart_to_retrieve_dnds.R, extract mouse-rat orthologous genes.
• src_mouse_human_biomart_to_retrieve_dnds.R, extract mouse-human orthologous genes.
• src_GOterms_map2_mouse.genes_BP.CC.MF.R, extract GO terms and their assocaited gene members in mice.