Extended Data Fig. 5: CELLO-seq to study locus specific TE expression.
From: Locus-specific expression of transposable elements in single cells with CELLO-seq
(a) Heatmap of expression of all SINE elements in mouse blastomeres, with rows clustered by SINE family and colour-coded by TE subfamily. (b) Heatmap of expression of full-length (>5000nt) elements in mouse blastomeres, with rows clustered by TE family and color-coded by TE subfamily. (c) Heatmap of logcounts of highest expressed (mean expression > 1) elements in hiPSCs with rows clustered by TE subfamily. (d) Boxplot of percentage of reads mapped to TEs or TE families in CELLO-seq mouse 2-cells. P-value: L1Md to SINE B1/B2 = 0.004998, L1Md to MERVL = 0.004998, 2-sided Wilcoxon rank sum test. n = 6 cells. (e) Boxplot of percentage of TEs expressed by number of TEs in the genome in CELLO-seq mouse blastomeres. p-value: repeats to L1Md = 0.0022, repeats to SINE B1/B2 = 0.0022, repeats to MERVL = 0.0022, 2-sided Wilcoxon rank sum test. n = 6 cells. (f) boxplot of number of MERVL elements expressed in each cell of CELLO-seq 2-cells compared to published short read data. CELLO-seq (n = 6 cells), bulk (n = 7 independent experiments). (g) boxplot of number of HERVH-int elements expressed in each cell of CELLO-seq compared to published short read data. CELLO-seq (n = 96 cells), bulk (n = 10 independent experiments). (h) expression, methylation, ATAC-seq and ChIP-seq of MERVL elements with read counts in CELLO-seq libraries compared to MERVL elements with no counts in CELLO-seq libraries. expressed (n = 355 MERVLs), not expressed (n = 41 MERVLs), datasets: ATAC-seq (n = 1), DNA methylation (n = 2), H3K27me3 (n = 1), H3K4me3 (n = 1), H3K9me3 (n = 1), RNAseq (n = 3). (i) expression, methylation, ATAC-seq and ChIP-seq data of HERV-int elements with read counts in CELLO-seq libraries compared to HERVH-int with no counts in CELLO-seq libraries. expressed (n = 14 HERVH-ints), not expressed (n = 110 HERVH-ints), each dataset (n = 1), RNAseq (n = 3). The boxplots shown in D-I show the median, first and third quartiles as a box, and the whiskers indicate the most extreme data point within 1.5 lengths of the box.
