REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-β-actin	Santa Cruz Biotechnology	Cat#SC-47778; RRID: AB_626632
anti-Myc-tag	Santa Cruz Biotechnology	Cat#SC-40; RRID:AB_627268
anti-SQSTM1/p62	Santa Cruz Biotechnology	Cat#SC-28359 ; RRID: AB_628279
anti-LC3B	Cell Signaling Technology	Cat#3868S; RRID: AB_2137707
anti-ATG4B	Cell Signaling Technology	Cat#5299S; RRID: AB_10622184
anti-phosphor-Histone H2A.X (Ser139)	Cell Signaling Technology	Cat#9718S; RRID:AB_2118009
anti-Myc-Tag (Sepharose bead conjugate)	Cell Signaling Technology	Cat#3400S; RRID: AB_10692357
anti-ATG4A	Cell Signaling Technology	Cat#7613S; RRID: AB_10827645
anti-CD44	Cell Signaling Technology	Cat#3570S; RRID: AB_10693293
anti-SOX2	Cell Signaling Technology	Cat#3579S; RRID:AB_2195767
anti-MST1	Cell Signaling Technology	Cat#14946
anti-MST2	Cell Signaling Technology	Cat#3952; RRID: AB_10694853
anti-ATG4C	Cell Signaling Technology	Cat#5262S; AB_10626627
anti-phosphor-AKT (Ser473)	Cell Signaling Technology	Cat#4060S; RRID: AB_2315049
anti-AKT	Cell Signaling Technology	Cat#9272S; RRID: AB_329827
anti-phospho-p44/42 MAP kinase Thr202/Tyr204	Cell Signaling Technology	Cat#9101S; RRID:AB_331646
anti-p44/42 MAP kinase	Cell Signaling Technology	Cat#9102S; RRID:AB_330744
anti-cleaved Caspase-3 (Asp175)	Cell Signaling Technology	Cat#9661S; RRID:AB_2341188
anti-ATG7	Cell Signaling Technology	Cat# 8558, RRID:AB_10831194
anti-ATG5	Cell Signaling Technology	Cat# 12994, RRID:AB_2630393
anti-ATG4D	Proteintech Group	Cat#16924-1-AP;RRID:AB_2062024
anti-MST4 (for IB, IHC and IF)	Abcam	Cat#ab52491; RRID:AB_881249
anti-p-S383-ATG4B	Abmart	NA
anti-ATG4B	Abmart	NA
anti-Flag	Sigma-Aldrich	Cat#F3165;RRID:AB_259529 Cat#F7425; RRID:AB_439687
anti-p-Ser	Thermo Fisher Scientific	Cat# 61-8100, RRID:AB_2533940
Peroxidase-IgG Fraction Monoclonal Mouse Anti-Rabbit IgG, Light Chain Specific	Jackson ImmunoResearch Laboratories	Cat# 211-032-171; RRID:AB_2339149
anti-Ki-67	EMD Millipore	Cat#AB9260, RRID:AB_2142366
Alexa Fluor 488	Thermo Fisher Scientific	Cat# A-11008, RRID:AB_143165
Alexa Fluor 594	Thermo Fisher Scientific	Cat# R37117, RRID:AB_2556545
Horseradish Peroxidase Streptavidin antibody	Vector Laboratories	Cat# SA-5004, RRID:AB_2336509
Anti-Mouse IgG (H+L), rat adsorbed, made in horse antibody	Vector Laboratories	Cat# BA-2001, RRID:AB_2336180
Biotinylated Goat Anti-Rabbit IgG antibody	Vector Laboratories	Cat# BA-1000, RRID:AB_2313606
anti-Rabbit Immunoglobulins	DAKO	Cat# P0217
anti-Mouse Immunoglobulins	DAKO	Cat# P0260
anti-Goat Immunoglobulins	DAKO	Cat# P0449
Biological Samples
Paraffin-emended GBM tissue	Saitama Medical University	Saitama, Japan
Chemicals, Peptides, and Recombinant Proteins
Chloroquine (CQ)	Sigma	Cat#C6628
NSC185058	NCI Developmental Therapeutics Program	NIH, NCI, USA
AquaBlock	East Coast Bio	Cat#PP82
Propidium Iodide	BD Biosciences	Cat#556463
Annexin V-APC	BD Biosciences	Cat#550475
Vybrant™ DyeCycle™ Violet Stain	Thermo Fisher Scientific	Cat#V35003
S-Adenosyl Methione	New England Biolabs	Cat#B9003S
DNA methyltransferase	New England Biolabs	Cat#M0230S
BsmBI	New England Biolabs	Cat#R0580S
Vectashield mounting medium with DAPI	Vector Laboratories	Cat#H-1200
Bsh1236I (BstUI)	Thermo Fisher Scientific	Cat#ER0921
Hesperadin	Selleckchem	Cat#S1529
PD98059	Selleckchem	Cat#S1177
Lipofectamine 2000	Thermo Fisher Scientific	Cat#11668019
Kinase buffer	Cell Signaling Technology	Cat#9802
ATP	Cell Signaling Technology	Cat#9804
D-Luciferin	Gold Bio	Cat#LUCK
Peanut oil	Sigma-Aldrich	Cat#2144
Protease Inhibitor Cocktail	Sigma-Aldrich	Cat# 11836153001
Phosphatase inhibitor	Sigma-Aldrich	Cat# 4906837001
Protein G Agarose	Sigma-Aldrich	Cat# 16-266
2% paraformaldehyde/2.5% glutaraldehyde	Polysciences	Cat#22872
IP Lysis Buffer	Thermo Fisher Scientific	Cat#87788
O.C.T Compound	Thermo Fisher Scientific	Cat#23-730-571
Critical Commercial Assays
QuikChange mutagenesis kit	Agilent Technologies	Cat#200515-5
CellTiter Glo 2.0	Promega	Cat#G9241
Epitech bisulphite conversion kit	Qiagen	Cat#59104
QIAquick Gel Extraction kit	Qiagen	Cat#28704
Deposited Data
GSC microarray	Mao et al., 2013	GSE67089; (Mao et al., 2013)
GSC 450K DNA methylation array	This and another studies	Deposited to GEO as GSE90948.
Experimental Models: Cell Lines
M83	Mao et al., 2013	N/A
1123	Mao et al., 2013	N/A
30	Mao et al., 2013	N/A
528	Mao et al., 2013	N/A
17	Mao et al., 2013	N/A
19	Mao et al., 2013	N/A
84	Mao et al., 2013	N/A
157	Mao et al., 2013	N/A
HEK293T	ATCC	ATCC CRL-3216
JK42	Srikanth et al., 2013	N/A
JK83	Srikanth et al., 2013	N/A
JK44	Srikanth et al., 2013	N/A
JK46	Srikanth et al., 2013	N/A
JK18	Srikanth et al., 2013	N/A
JK34	Srikanth et al., 2013	N/A
JK92	Srikanth et al., 2013	N/A
JK16	Srikanth et al., 2013	NA
23	Bhat et al., 2013	NA
543	Rohle et al., 2013	N/A
600	Rohle et al., 2013	N/A
Experimental Models: Organisms/Strains
Athymic (Ncr nu/nu) mice	Taconic Farms	N/A
Oligonucleotides
lentiCRIPSRv2GFP-STK26-KO-1 construction primers: F: CACCGTTGGACAGCCACCGGCGAGT R: AAACACTCGCCGGTGGCTGTCCAAC	IDT	N/A
lentiCRIPSRv2GFP-STK26-KO-2 construction primers: F: CACCGCCGGTGGCTGTCCAAGTGCC R: AAACGGCACTTGGACAGCCACCGGC	IDT	N/A
STK26 genomic DNA sequencing primer: F: CTCTTCCTAAAGCGGCGAGG R: CAGCATTTCTCACGCCACAC	IDT	N/A
Recombinant DNA
TRC shRNA Control	Dharmacon	Cat#RHS6848
GIPZ shRNA Control	Dharmacon	Cat#RHS4346
ATG4B shRNA #1	Dharmacon	TRCN0000073798
ATG4B shRNA #4	Dharmacon	TRCN0000073801
ATG4B shRNA #5	Dharmacon	TRCN0000073802
ATG4B shRNA (Target 3’UTR)	Dharmacon	V3SH7591-225104933
MST4 shRNA #1	Dharmacon	TRCN0000003192
MST4 shRNA #2	Dharmacon	TRCN0000003193
MST4 shRNA (Target 3’UTR)	Dharmacon	V3SH7590-225006062
ATG5 shRNA	Dharmacon	V2LHS_248503
ATG7 shRNA	Dharmacon	V2LHS_13452
pCDH-MST4 WT and mutants	This study	N/A
pCDH-MST4 K53E	This study	N/A
pCDH-MST4 T178A	This study	N/A
pCDH-ATG4B WT	This study	N/A
pCDH-ATG4B C74S	This study	N/A
pCDH-ATG4B S383A	This study	N/A
pCDH-ATG4B S383D	This study	N/A
pcDNA-myc-MST4 WT	This study	N/A
pcDNA-myc-MST4 K53E	This study	N/A
pcDNA-Flag-ATG4B WT and domain deleted mutants	(Kuang et al., 2012)	N/A
pcDNA-Flag-ATG4B S383A	This study	N/A
pcDNA-mycMST4 1-279/280-416	This study	N/A
lentiCRISPRv2GFP	(Walter et al., 2017)	Addgene #82416
psPAX2	Didier Trono	Addgene #12260
pCMV-VSV-G	(Stewart et al., 2003)	Addgene #8454
pET28a -ATG4B WT and C74S	(Li et al., 2011)	(Li et al., 2011)
pET28a -FRET-LC3B	(Li et al., 2012)	(Li et al., 2012)
Software and Algorithms
Firebrowse		http://firebrowse.org/
Betastasis		www.betastasis.com/glioma/tcga_gbm/
gRNA design MIT on line tool		http://crispr.mit.edu
Other
PrepEase	USB	Cat# P-78796B
Superdex 75 column	GE Health	Cat# 1068-01
pGEM-T	Promega	Cat#: A3600