with • Iden6fy expressed regions with derfinder – Adjust coverage (40 million) – Find expressed regions (cutoff 5) – Discard ERs < 9 bp GTEx: DERs via expressed regions
~2 million paired-end reads for chr17 1/6 high, 1/6 low in group 2 vs group 1 Annota6on: complete missing 20% of transcripts (8.28% exons) Reference set: 3868 exons that overlap only 1 transcript
6 / group, N = 36 Discovery data Null: Alt: Models Initial results Jaffe et al, Nat. Neuroscience, 2015 50,650 DERs replicated 63,135 DERs Final results
N 1 call peaks call peaks call peaks U 11 U 12 U 1N Number of unique peaks Merge unique peaks Total peaks: U merged ≤ U 1 + U 2 Determine differentially bound peaks between groups 1 & 2 Total tests: U merged 1 Total: U 1 Sample 1 Sample 2 ... Sample N 2 call peaks call peaks call peaks U 21 U 22 U 2N Number of unique peaks 2 Total: U 2 Group 1 Group 2 (A) (A) (B) (C)
Cell type Age at death 0 1 14604 209 0 0 48 0 H3K27ac DBRs by main covariates Brain region Cell type Age at death 0 2 178869 1235 0 0 156 0 H3K4me3 H3K27ac
change expression during brain development 1. derfinder permits discovery of novel expressed & differen6ally bound regions 2. we iden6fied & validated gene expression changes in the developing brain 3. we have developed tools for reproducible shareable repor6ng 4. these tools can be easily be used to process 2,040 projects via recount
Battle Andrew Jaffe Hongkai Ji Fernando Pineda Collaborators Alyssa Frazee Abhinav Nellore Michael Love Ben Langmead Rafael Irizarry Funding NIH LIBD JHU-Biostats CONACyT México