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. Author manuscript; available in PMC: 2021 Jul 30.
Published in final edited form as: Cell Rep. 2021 Jun 29;35(13):109321. doi: 10.1016/j.celrep.2021.109321
REAGENT or RESOURCE SOURCE IDENTIFIER
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