KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, Peptides and Recombinant Proteins
DMEM, high glucose, pyruvate	ThermoFisher Scientific	SKU#11995–065
Fetal Bovine Serum	Atlanta Biologicals	Cat#S11150
NEBNext Poly(A) mRNA Magnetic Isolation Module	New England Biolabs	Cat#E7490S
Fast Evagreen qPCR Master Mix	Biotium	Cat#31003
Opti-MEM Reduced Serum Medium	Invitrogen	Cat#22600050
Lipofectamine LTX Reagent with PLUS Reagent	Invitrogen	Cat#A12621
RNeasy	QIAGEN	Cat#74104
PolyA Spin mRNA Isolation Kit	New England Biolabs	Cat#S1560
MultiScribe Reverse Transcriptase	Invitrogen	Cat#4311235
Deposited Data
5’ Alternative Splicing MPRA	This study and Rosenberg et al., 2015	https://github.com/johli/splirent
APA Reporter Plasmids (qPCR Assay)	This study	https://github.com/johli/genesis/tree/master/analysis/apa/qpcr_experiment
Experimental Models: Cell Lines
HEK293FT	Invitrogen	Cat#R70007
HELA	ATCC	Cat#CCL-2.2
MCF7	ATCC	Cat#HTB-22
CHO-K1	ATCC	Cat#CCL-61
Software and Algorithms
DEN Software & Analysis	This study	https://github.com/johli/genesis
APA Predictor Software	Bogard et al., 2019	https://github.com/johli/aparent
Splicing Predictor Software	This study	https://github.com/johli/splirent
Feedback-GAN Software	Gupta and Zou, 2019	https://github.com/av1659/fbgan
CbAS Software & Benchmark	Brookes et al., 2019	https://github.com/dhbrookes/CbAS/
MPRA-DragoNN Software	Movva et al., 2019	https://github.com/kundajelab/MPRA-DragoNN
DragoNN (SPI1) Software	Kundaje Lab	https://github.com/kundajelab/dragonn