Fig. 3

RNA sequencing of transferred 5-ethynyl uridine (EU)-labelled transcripts. a Volcano plot from RNA sequencing data of EU-labelled transferred transcripts affinity precipitated from endometrial cells co-incubated with EU-labelled trophoblast spheroids. RNA extracted from endometrial cells co-incubated with unlabelled spheroids were used as negative control. The rate of false discovery is plotted against fold change, demonstrating the 18 putatively transferred transcripts which were significantly enriched in experimental group (black dots). Candidate transferred transcripts were highlighted by red dots (ZNF81 and LINC00478). b Heatmap displaying the relative abundances of transcripts enriched in the experimental group compared to the negative control. The values presented on the heatmap are z-scores calculated based on the normalized read counts. Unsupervised hierarchical clustering of samples based on Euclidean distance calculated from presented z-scores is displayed alongside the heatmap. c Position of enriched intronic- LINC00478 and exonic- LINC00478 in relation to chromosome 21. d Position of enriched ZNF81 in relation to chromosome X. Copy number of EU-labelled (e) Intronic-LINC00478 (f) Exonic-LINC00478 and (g) ZNF81 were measured in endometrial cells co-incubated with EU-labelled trophoblast spheroids (Experimental group) by using qPCR and absolute quantification. Endometrial cells co-incubated with unlabelled trophoblast spheroids were used as a control (Negative control). Data is presented as mean ± SEM. (*) p < 0.05 vs negative control. h Presence of intronic-LINC00478 was observed in EU-labelled spheroid/endometrial cell co-culture conditioned media (Experimental group, E-CM) and extracted EVs (Experimental group, E-EV), and in EU-unlabelled spheroid/endometrial cell co-culture conditioned media (Negative control, NC-CM). Exonic-LINC00478 and ZNF81 were not detected in either group. Data is presented as mean ± SEM