Number of reads deviating from starting position in ERCC control molecules shown as percent of reads mapping exactly to the starting position. The number in red shows total number of ERCC molecules participating in libraries for CA1 neurons. Note that the scale is broken.
Read distribution across genes, shown as percent mapped reads (after UMI correction) in 20 length‐bins for CA1 neurons (top) and ERCC control RNA (bottom).
Read distribution for CA1 neurons. A read is only assigned once to one of the four groups.
CA1 neuron reads mapped to the region ± 100 bp from the TSS, defined as the center of CAGE‐annotated TSSs.
Major TSS preference in pooled single cells from CA1 neurons.
Correlation of major TSS expression in pooled single CA1 neurons.
Correlation of whole‐gene expression in individual single CA1 neurons.
Correlation of major TSS expression in individual single CA1 neurons.
Data information: (F–H) Pearson correlation values in red.
Figure 2.Correlated expression of major and minor TSS in single cells
Illustration of two models for TSS expression in single cells versus their common effect on the population expression.
Examples of TSS expression in single CA1 neuron cells. Plots show the number of mRNA molecules detected from the major and minor TSSs in single cells. Each dot is a single cell. Pearson correlation values are indicated in red. Four examples are shown, representing high and low expression, and high and low correlation.
Distribution of correlation values showing effect of TSS distance. Histogram based on 197 genes with an expression of at least 0.3 molecules per cell per TSS for CA1 neurons. Genes were divided based on major/minor TSS distance (“TSS”, 186 genes with < 1 kb inter‐TSS distance; “Promoters”, 11 genes with > 1 kb TSS distance).
Average correlation between major/minor TSS as a function of TSS distance. Colors represent TSSs and promoters as in (C). The error bars show standard deviation and the numbers in brackets show participating genes.
Scatterplot showing total expression (horizontal axis) and major/minor TSS correlation coefficient (vertical). Each dot is a gene. Colors represent genes with “TSS” and “Promoter” TSSs as in (D). Four example genes from (B) are marked in the plot. Linear regression lines are shown with P‐values of the fit.
Percentage of cells that significantly deviates from expected major to minor TSS ratio as a function of cell gene expression. Percentage of deviating cells were calculated using the binomial test. Each dot represents a gene.
Scatterplot showing total expression (horizontal axis) and major/minor TSS correlation coefficient (vertical). Each dot is a gene. Colors represent genes with “TSS” and “Promoter” TSSs.
Examples of TSS expression in single CA1 neuron cells. Plots show the number of mRNA molecules detected from the major and minor TSSs in single cells. Each dot is a single cell. Pearson correlation values are indicated in red.
Promoter expression of genes with TSS pairs expressed from different exons using the UCSC genome browser. Expression is shown as bars where the y‐axis for single cells has a limit of five molecules and for all cells combined has a limit of 500 molecules. Major and minor TSSs are marked in red, while other CAGE peaks associated with a gene are marked in black.