Additional file 2 of Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels

Additional file 2: Figure S2. (A) Plot of RNA-Seq reads from 3 EV and 3 cell samples that map to more than one genomic location. Reads mapping to rRNA are excluded. Individual values can be found in Additional file 17. (B) Hierarchical clustering of long RNA transcripts by abundance determined by RNA-Seq in 3 EV and 3 cell samples. Data are read counts transformed using the Variance Stabilizing Transformation, top 200 transcripts with the highest variance across samples are displayed. (C) RNA-Seq read coverage (top) and RT-PCR amplicons (bottom) of HNRNPA1 (D), ANP32B (E), RPL14 (F) and RPL41 (F) mRNA. (G) RNA-Seq read coverage (top) and RT-PCR amplicons (bottom) of lncRNA GAS5. NT = no template, no-RT = RNA without reverse transcriptase. Uncropped gel images can be found in Additional file 18

Additional file 11 of Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels

Additional file 11. Fold changes, adjusted p-values and TPMs for genes in tumor-exposed, CD31-selected cells and their EVs

Additional file 12 of Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels

Additional file 12. Fold changes, adjusted p-values and TPMs for genes in CD31-selected cells exposed to tumor cells or not

Additional file 6 of Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels

Additional file 6: Figure S5. (A) mRNA and (B) lncRNA abundance from RNA-Seq in VEGF-treated cells and their EVs. TPM = transcripts per million. TPM values are averaged across 3 replicates. (C) Gene Ontology analysis of genes altered in cells by VEGF treatment. For each GO category the ten significant (FDR < 0.05) terms with the lowest p-values are displayed. BP = Biological Process, CC = Cellular Component, MF = Molecular Function. Individual values can be found in Additional file 17. (D) Volcano plot of log2 fold changes by RNA-Seq of mRNA and lncRNA genes (combined) in EVs derived from VEGF-treated cells vs. EVs derived from untreated cells. (E) Volcano plot of log2 fold changes by RNA-Seq of mRNA and lncRNA genes in VEGF-treated cells vs. untreated cells. All analyses were performed using 3 EV and 3 cell samples

Additional file 10 of Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels

Additional file 10. Fold changes, adjusted p-values and TPMs for genes in CD31-selected cells and EVs

Additional file 18 of Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels

Additional file 18. Uncropped gels and blots

Additional file 4 of Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels

Additional file 4: Figure S3. (A) EV enrichment/depletion of expressed antisense (AS) genes and their protein-coding (PC) complements. Red = significantly enriched or depleted antisense gene. Blue = significantly enriched or depleted protein-coding gene. Purple = both antisense gene and protein-coding gene are significantly enriched/depleted. Padj < 0.1 for significance. N = 5526 expressed protein-coding/antisense gene pairs. (B) EV enrichment/depletion of expressed long intergenic noncoding RNA (lincRNA) genes and the nearest protein-coding genes. Red = significantly enriched or depleted lincRNA. Blue = significantly enriched or depleted protein-coding gene. Purple = both lincRNA and neighboring protein-coding gene are significantly enriched/depleted. Padj < 0.1 for significance. N = 7592 expressed lincRNA/neighboring protein-coding gene pairs. (C—F) Violin plots of mRNA transcript length (C), 5’UTR length (D), CDS length (E), 3’UTR length (F) for EV-enriched (n = 609) and EV-depleted (n = 680) protein-coding genes. (G) Violin plot of lncRNA transcript length for EV-enriched (n = 72) and EV-depleted (n = 123) lncRNA genes. (H-I) Violin plots of number of exons per kilobase of transcript length for EV-enriched and EV-depleted protein-coding (H) or lncRNA genes (I). (J) Violin plot of transcript half-life in 4SU-labeled LCLs for EV-enriched and EV-depleted transcripts (K) Violin plot of transcript half-life in HeLa cell BRIC-Seq for EV-enriched and EV-depleted transcripts (L) Violin plot of transcript half-life in Actinomycin D-treated A673 cell RNA-Seq for EV-enriched and EV-depleted transcripts. For all violin plots, medians are indicated above each violin and grey dotted lines indicate median of all expressed genes. P-values calculated by Welch two-sample t-test are indicated. (M-N) Plots of occurrences of ARE elements per kilobase of transcript in 3’ UTRs (M) and 5’ UTRs (N) of EV-enriched and EV-depleted transcripts. Individual values can be found in Additional file 17. All analyses were performed using 3 EV and 3 cell samples. All p-values for differences are calculated by Welch two-sample t-test

Additional file 8 of Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels

Additional file 8. Fold changes, adjusted p-values and TPMs for genes in cells treated with VEGF or not

Additional file 19 of Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels

Table S1. PCR primer

Additional file 14 of Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels

Additional file 14: Figure S6. (A) Gene Ontology analysis of protein-coding genes altered in cells by coculture. For each category the top 10 most significantly enriched GO terms (FDR < 0.05) are displayed. BP = Biological Process, CC = Cellular Compartment, MF = Molecular Function. Individual values can be found in Additional file 17. (B) Volcano plot of log2 fold changes by RNA-Seq of mRNA and lncRNA genes (combined) in EVs derived from tumor-exposed cells vs. EVs derived from unexposed cells. (C) Log2 fold change in tumor-exposed cells vs. unexposed cells and in EVs derived from tumor-exposed cells vs. EVs derived from unexposed cells for the most increased (left) and decreased (right) mRNA and lncRNA genes significantly changed in cells. Error bars represent standard error of log2 fold change. Individual values can be found in Additional file 17. (D-E) Depletion of E2F_TARGETS_V1 gene set (D) and G2M_TARGETS gene set (E) in tumor-exposed vs. unexposed cells and enrichment of the same gene set in EVs derived from tumor-exposed vs. unexposed cells. All analyses were performed using 3 EV and 3 cell samples