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
|