Antibodies |
PARP |
Cell Signaling Technology |
Cat# 9542; RRID:AB_2160739 |
Celaved Caspase-3 (D175) |
Cell Signaling Technology |
Cat# 9661; RRID:AB_2341188 |
eIF4E |
BD |
Cat# 610270; RRID:AB_397665 |
p-eIF4E Ser209 |
Cell Signaling Technology |
Cat# 9721; RRID:AB_561095 |
beta-Actin |
Sigma-Aldrich |
Cat# A5316; RRID:AB_476743 |
Pmpcb |
Protein Tech |
Cat# 16064-1-AP; RRID:AB_2167122 |
Tfeb |
Bethyl Laboratories |
Cat# A303-673A; RRID:AB_11204751 |
a-Tubulin |
Sigma-Aldrich |
Cat# T8203; RRID:AB_1841230 |
LC3A/B |
Cell Signaling Technology |
Cat# 4108; RRID:AB_2137703 |
c-Myc (D84C12) |
Cell Signaling Technology |
Cat# 5605; RRID:AB_1903938 |
Ras |
Cell Signaling Technology |
Cat# 3965; RRID:AB_2180216 |
Atf4 (D4B8) |
Cell Signaling Technology |
Cat# 11815; RRID:AB_2616025 |
Xbp-1 |
Abcam |
Cat# Ab37152; RRID:AB_778939 |
Magoh |
Protein Tech |
Cat# 12347-1-AP; RRID:AB_2265988 |
eIF4AIII/eIF4A3 |
Bethyl Laboratories |
Cat# A302-981A; RRID:AB_10748369 |
Rbm8a |
Bethyl Laboratories |
A301-033A; RRID:AB_2300943 |
Bcl-xL (H5) |
Santa Cruz |
Cat# sc-8392; RRID:AB_626739 |
Bacterial and virus strains |
MegaX DH10B T1R Electrocomp Cells |
Thermo Fisher Scientific |
C640003 |
Chemicals, peptides, and recombinant proteins |
A-1331852 |
MedChemExpress |
HY-19741 |
eFT508 |
eFFECTOR Therapeutics |
Trizol |
Sigma-Aldrich |
T9424-200ML |
Trizol LS |
Invitrogen |
10296010 |
Matrigel |
Corning |
CB40234 |
PhosSTOP |
Roche |
4906837001 |
Complete Mini proteosome inhibitors |
Roche |
11836170001 |
Glycogen |
Roche |
10901393001 |
Paraformaldehyde |
Poly-lysine |
Sigma |
P4707-50ML |
Critical commercial assays |
FITC-Annexin V |
Thermo Fisher Scientific |
A13199 |
UPRmt TF Activation Profiling |
Signosis |
FA-1010 |
Cell Titer Glo |
Promega |
G9241 |
Polybrene |
Millipore Sigma |
TR-1003-G |
Lipofectamine 2000 |
Thermo Fisher Scientific |
11662019 |
Lipofectamine LTX |
Thermo Fisher Scientific |
15338100 |
TOPO-TA |
Invitrogen |
450641 |
Super Signal West Pico Plus Chemiluminescent substrate |
Thermo Scientific |
34580 |
NE-PER Nuclear and Cytoplasmic Extraction Reagents |
Thermo Scientific |
78835 |
Direct-zol RNA Microprep |
Zymo Research |
R2061 |
High-Capacity cDNA Reverse transcription kit |
Applied Biosystems |
4368814 |
PowerUP SYBR Green master mix |
Applied Biosystems |
A25741 |
TurboDNA-free kit |
Invitrogen |
AM1907 |
Dual-luciferase Reporter Assay System |
Promega |
E1910 |
SuperScript III first-strand synthesis kit |
Invitrogen |
18080044 |
Prolong Diamond Antifade mountant with DAPI |
Invitrogen |
P36971 |
Ribo-Zero |
Illumina |
20040526 |
ScriptSeq v2 RNA-seq library preparation kit |
Epicenter |
SSV21124 |
Deposited data |
RNA seq Data |
This paper |
GEO: GSE175417
|
Experimental models: Cell lines |
MEFs eIF4E+/−
|
This paper |
|
Oligonucleotides |
See Table S3
|
This paper |
|
Recombinant DNA |
pBabe-Neo-LargeT |
Hahn et al., 2002 |
Addgene #1780 |
pCL-Eco |
Naviaux et al., 1996 |
Addgene #12371 |
pX458 |
Ran et al., 2013 |
Addgene #48138 |
human HRASV12
|
Serrano et al., 1997 |
Addgene #18749 |
human c-Myc |
Boehm et al., 2005 |
Addgene #10674 |
psPAX2 |
Didier Trono |
Addgene #12260 |
pMD2.G |
Didier Trono |
Addgene #12259 |
pLKO.1 |
Stewart et al., 2003 |
Addgene #8453 |
pMSCV |
Clontech |
634401 |
pGL3 |
Promega |
E1751 |
pRL |
Promega |
E2231 |
pLG15 |
Luke Gilbert |
|
sgRNA expressing vectors |
This paper |
|
pMSCV-GFP-Tfeb |
This paper |
|
pMSCV-GFP-Pmpcb |
This paper |
|
TFEB 5’UTR containing pGL3 reporters |
This paper |
|
mouse CRIPSRi library expressing 5 sgRNAs for each gene |
IGI CRISPR screening core at UCSF |
|
Software and algorithms |
ImageJ |
|
https://imagej.nih.gov/ij/ |
Fiji |
|
https://imagej.net/software/fiji |
ImageLab software |
BioRad |
|
Prism |
GraphPad |
Version 9.1.0 |
R Studio |
|
https://www.rstudio.com/ |
HISAT v2.0.5 |
|
http://daehwankimlab.github.io/hisat2/ |
RSEM v1.3.0 |
|
https://github.com/deweylab/RSEM/releases
|
DAVID v6.8 |
|
https://david.ncifcrf.gov/ |
‘survminer’ R package |
|
https://github.com/kassambara/survminer |
AdobePhotoshop |
Adobe |
|
Adobe Illustrator |
Adobe |
|