Additional file 16: of RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking

IRB approval and complete list of acknowledgements. (DOCX 20 kb

Additional file 13: Figure S9. of RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking

Exon-level expression of MAN1A2. The top plot shows mean normalized counts by smoking status on the log scale for each analyzed exon. One exon that showed significant differential usage (ENSE00001635177). The bottom table maps tested exons to known transcripts (1 = exon present in that transcript, 0 = exon not present in that transcript). (PNG 51 kb

Additional file 8: Figure S4. of RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking

Quantile-quantile (QQ) plot for differential exon usage between current and former smokers using the topSplice exon-based T-statistic. (PNG 16 kb

Additional file 10: Figure S6. of RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking

Exon-level expression of SASH1. The top plot shows mean normalized counts by smoking status on the log scale for each analyzed exon. One exon showed significant differential usage (ENSE00001444573). The bottom table maps tested exons to known transcripts (1 = exon present in that transcript, 0 = exon not present in that transcript). (PNG 64 kb

Additional file 9: Figure S5. of RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking

Exon-level expression of EPS15. The top plot shows mean normalized counts by smoking status on the log scale for each analyzed exon. One exon showed significant differential usage (ENSE00001810132). The bottom table maps tested exons to known transcripts (1 = exon present in that transcript, 0 = exon not present in that transcript). (PNG 92 kb

Additional file 6: Table S3. of RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking

Significant gene ontology terms over-represented in genes differentially expressed between current and former smokers. P-values are Bonferroni corrected for multiple comparisons. (XLSX 16 kb

Additional file 4: Figure S2. of RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking

Quantile-quantile (QQ) plots for differential gene expression analysis between current and former smokers using voom/limma. (PNG 14 kb

Additional file 1: Figure S1. of RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking

Gene annotation of 27,885 observed genes (Ensembl version 81 annotation). (PNG 19 kb

Additional file 12: Figure S8. of RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking

Exon-level expression of last 11 exons of UTRN. The top plot shows mean normalized counts on the log scale for each exon passing filtering by smoking status. There was one exon that showed significant differential usage between current and former smokers (ENSE00001444981). The bottom table maps tested exons to known transcripts (1 = exon present in that transcript, 0 = exon not present in that transcript). (PNG 141 kb

Additional file 14: Figure S10. of RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking

Exon-level expression of LRRN3. The top plot shows mean normalized counts by smoking status on the log scale for each analyzed exon. One exon showed significant differential usage between current and former smokers (ENSE00001231507). The bottom table maps tested exons to known transcripts (1 = exon present in that transcript, 0 = exon not present in that transcript). (PNG 46 kb