Reagents and tools table

Primary antibodies
Name	Dilution	Source	Catalog number
Anti-Cleaved Notch1 (Val1744) (D3B8) rabbit mAB	1:1000 (WB)	Cell Signaling Technology	4147 (RRID:AB_2153348)
Anti-Cyclin D1, mouse mAB	1:1000 (WB)	BD Biosciences	556470 (RRID: AB_396432)
Anti-GFAP antibody, chicken pAB	1:500 (IF)	Millipore	AB5541 (RRID: AB_177521)
Anti-GFP antibody, chicken pAB	1:500 (IF)	Abcam	ab13970 (RRID: AB_300798)
Anti-Ki67, rabbit pAB	1:200 (FC)	Abcam	ab15580 (RRID:AB_443209)
Anti-p27Kip1, mouse mAB	1:1000 (WB); 1:300 (IF)	BD Biosciences	554069 (RRID:AB_395225)
Anti-SOX2, rabbit pAB	1 :1000 (WB)	Millipore	AB5603 (RRID:AB_2286686)
Anti-Sox9 (D8G8H), rabbit mAB	1:1000 (WB); 1:500 (IF)	Cell Signaling Technology	82630 (RRID:AB_2665492)
Anti-α-Tubulin, mouse mAB	1:10000 (WB)	Sigma Aldrich	T9026 (RRID:AB_477593)
Anti-Tubulin b3 (TUBB3), mouse mAB	1:500 (IF)	Biolegend	801201 (RRID:AB_2313773)
Secondary antibodies
Name	Dilution	Source	Catalog number
Anti-mouse IgG Alexa Fluor 647	1:1000	Invitrogen	A-21245
Anti-mouse IgG Alexa Fluor Plus 488	1:1000	Invitrogen	A-32723
Anti-mouse IgG HRP-linked	1:5000	Cell Signaling Technology	7076S
Anti-rabbit IgG Alexa Fluor 488	1:1000	Invitrogen	A-11034
Anti-rabbit IgG HRP-linked	1:5000	Cell Signaling Technology	7074S
Donkey anti-rabbit IgG (H + L), CF647	1:1000	Sigma	SAB4600177
Goat anti-rabbit IgG (H + L), Alexa Fluor 555	1:1000	Invitrogen	A-21428
Goat anti-chicken IgY (H + L) secondary antibody, Alexa Fluor 488	1:1000	Invitrogen	A-11039

Oligonucleotides and other sequence-based reagents
shRNAs	Sequence	Targeting site
Mouse_Sox10_sh1	CCACGAGGTAATGTCCAACAT	Coding region (TRCN0000018985)
Mouse_Sox10_sh2	TTGCTCCAGCGATACCTTAAT	3’ UTR (TRCN0000244290)
Non-targeting shRNA	CAACAAGATGAAGAGCACCAA	NA
sgRNAs	Sequence
Human_SOX10_sg1	ATTCAGGCTCCGTCCTAACG
Human_SOX10_sg2	CGAGCTGGACCGCACACCTT
Human_SOX10_sg3	AGTCTCGGGCTGTCCGGCCA
Negative control	GCGCCAAACGTGCCCTGACGG
qPCR primers	Forward sequence	Reverse sequence
Human-SOX10	CTTTCTTGTGCTGCATACGG	AGCTCAGCAAGACGCTGG
Human-SOX9	AGCGAACGCACATCAAGAC	CTGTAGGCGATCTGTTGGGG
Human-LRIG1	GTGTCATCACCAACCACTTTGGC	GCAATCTGAGGGTTTGGGTGAC
Human-NRARP	CAAGGGCAACACGCAGGAGCT	CCGAACTTGACCAGCAGCTTCA
Human-HES5	TCCTGGAGATGGCTGTCAGCTA	CGTGGAGCGTCAGGAACTGCA
Human-TBP	GAACCACGGCACTGATTTTC	CCCCACCATGTTCTGAATCT
Mouse Sox10	GTGCCAGCAAGAGCAAGCCG	CTGCCTTCCCGTTCTTCCGCC
Mouse-Sox9	CACACGTCAAGCGACCCATGAA	TCTTCTCGCTCTCGTTCAGCAG
Mouse-Lrig1	TTCAGCCAACGCTACCCTCACA	TAAGCCAGGTGATGCGTGGTGT
Mouse-Nrarp	CAGACAGCACTACACCAGTCAG	CCGAAAGCGGCGATGTGTAGC
Mouse-Hes5	CCGTCAGCTACCTGAAACACAG	GGTCAGGAACTGTACCGCCTC
Mouse-Tbp	ACCGTGAATCTTGGCTGTAAAC	GCAGCAAATCGCTTGGGATTA

Public datasets	Source
Brain tumor stem cell bulk RNA-seq	Marques et al, 2021
TCGA-GBM (HG-U133A)	TCGA

Drug-screening compounds
Cat no.	Name	Pathways	Target	Receptor
T1952	MK-2206 dihydrochloride	Cytoskeletal signaling; PI3K/Akt/mTOR signaling	Akt	Akt1; Akt2; Akt3
T3132	SC66	Cytoskeletal signaling; PI3K/Akt/mTOR signaling	Akt inhibitor	Akt
T2492	Perifosine	Cytoskeletal signaling; PI3K/Akt/mTOR signaling	Akt inhibitor	Akt
T4489	AZD26	PI3K/Akt/mTOR signaling; cytoskeletal signaling	Akt inhibitor	Allosteric Akt
T1961	Vistusertib	Cytoskeletal Signaling; PI3K/Akt/mTOR signaling; MAPK	Akt inhibitor; mTOR inhibitor; PI3K inhibitor; S6 Kinase inhibitor	P-Akt (S473); mTOR; PI3Kα; pS6 (S235/236)
T1936	Alectinib	Angiogenesis; tyrosine kinase/adaptors; tyrosine kinase/adaptors	ALK inhibitor; tyrosine kinases inhibitor; VEGFR inhibitor	ALK; ALK (F1174L); ALK (R1275Q); INSR; VEGFR2 (KDR)
T1661	Crizotinib	Angiogenesis; tyrosine kinase/adaptors	ALK; c-Met/HGFR	ALK; c-Met
T16156	MT 63-78	PI3K/Akt/mTOR signaling	AMPK; mTOR	AMPK;mTORC1
T2235	Dactolisib	DNA damage/DNA repair; PI3K/Akt/mTOR signaling	ATM/ATR; mTOR; PI3K	ATR; mTOR (p70 S6K); p110α; p110γ; p110δ
T2509	Tozasertib	Cell cycle/checkpoint; chromatin/epigenetic	Aurora Kinase	Aurora A; Aurora B; Aurora C
T6315	MLN8054	Cell cycle/checkpoint; metabolism; angiogenesis; GPCR/G protein; chromatin/epigenetic; stem cells	Aurora kinase inhibitor; casein kinase inhibitor; PKA inhibitor; Src inhibitor	Aurora A; Aurora B; CK2; PKA; Lck
T6458	CYC116	Cell cycle/checkpoint; angiogenesis; PI3K/Akt/mTOR signaling; chromatin/epigenetic; tyrosine kinase/adaptors; MAPK	Aurora Kinase inhibitor; CDK inhibitor; FLT inhibitor; S6 Kinase inhibitor; VEGFR inhibitor	Aurora A; Aurora B; CDK2/CyclinE; CDK9/CyclinT; FLT3; p70 S6K; VEGFR2
T2358	ENMD2076	Cell cycle/checkpoint; angiogenesis; apoptosis; chromatin/epigenetic; tyrosine kinase/adaptors	Aurora kinase inhibitor; c-RET inhibitor;FLT inhibitor; Src inhibitor; VEGFR inhibitor	Aurora A; RET; FLT3; Src; VEGFR3/FLT4; Src
T2378	RGB-286638 free base	Cell cycle/checkpoint	CDK inhibitor	CDK1/cyclinB1; CDK2/cyclinE; CDK3/cyclinE; CDK4/cyclin D1; CDK9/cyclinT1; p35-CDK5
T2029	Bohemine	Cell cycle/checkpoint	CDK inhibitor	CDK
T2247	KenPaullone	PI3K/Akt/mTOR signaling; cell cycle/checkpoint; stem cells	CDK inhibitor; GSK-3 inhibitor	CDK1/CyclinB; CDK2/CyclinA; CDK2/CyclinE; CDK5/p35; GSK-3β
T1778	AT 7519 hydrochloride salt	PI3K/Akt/mTOR signaling; cell cycle/checkpoint; stem cells	CDK inhibitor; GSK-3 inhibitor	CDK2/CyclinA; CDK4/Cyclin D1; CDK5/p35; CDK9/CyclinT; GSK-3β
T4327	Prexasertib dihydrochloride	Cell cycle/checkpoint; PI3K/Akt/mTOR signaling; MAPK	Chk; S6 Kinase	Chk1;Chk2;RSK
T4301	AD80	Tyrosine kinase/adaptors; MAPK; angiogenesis; PI3K/Akt/mTOR signaling; apoptosis	c-RET; Raf; Src; S6 Kinase	RET, RAF, SRC, S6K;RET V804M;RET V804L
T3458	EED226	Chromatin/epigenetic	DNA methyltransferase inhibitor; Histone methyltransferase inhibitor	EED; PRC2
T2377	XL147 analogue	DNA damage/DNA repair; PI3K/Akt/mTOR signaling	DNA-PK inhibitor; PI3K inhibitor	DNA-PK; PI3Kα; PI3Kβ; PI3Kγ; PI3Kδ
T1826	Voxtalisib Analogue	DNA damage/DNA repair; PI3K/Akt/mTOR signaling	DNA-PK inhibitor; PI3K inhibitor	DNA-PK; PI3Kα; PI3Kβ; PI3Kγ; PI3Kδ
T14073	A-485	Chromatin/epigenetic	Epigenetic Reader Domain; Histone Acetyltransferase	CBP/p300;histone acetyltransferase
T2608	CHIR98014	PI3K/Akt/mTOR signaling; angiogenesis; stem cells; tyrosine kinase/adaptors; MAPK	FGFR inhibitor; GSK-3 inhibitor; S6 Kinase inhibitor; Src inhibitor	bFGFR; GSK-3α; GSK-3β; p70 S6K; c-Src
T2310	CHIR99021	PI3K/Akt/mTOR signaling; stem cells	GSK-3	GSK-3α; GSK-3β
T1741	AZD1080	PI3K/Akt/mTOR signaling; stem cells	GSK-3 inhibitor	GSK-3α; GSK-3β
T1755	LY2090314	PI3K/Akt/mTOR signaling; stem cells	GSK-3 inhibitor	GSK-3α; GSK-3β
T3067	Tideglusib	PI3K/Akt/mTOR signaling; stem cells	GSK-3 inhibitor	GSK-3β
T1881	AR-A014418	PI3K/Akt/mTOR signaling; stem cells	GSK-3 inhibitor	GSK-3β; GSK-3β
T1957	AZD2858	PI3K/Akt/mTOR signaling; stem cells	GSK-3 inhibitor	GSK-3
T6187	TDZD8	PI3K/Akt/mTOR signaling; stem cells	GSK-3 inhibitor	GSK-3β
T6059	GSK343	Chromatin/epigenetic	Histone methyltransferase inhibitor	EZH1; EZH2
T3057	UNC1999	Chromatin/epigenetic	Histone methyltransferase inhibitor	EZH1; EZH2
T1788	EPZ6438	Chromatin/epigenetic	Histone methyltransferase inhibitor	EZH2; EZH2
T4583	(R)-PFI-2 hydrochloride	Chromatin/epigenetic	Histone methyltransferase inhibitor	SETD7
T1841	UNC0379	Chromatin/epigenetic	Histone methyltransferase inhibitor	SETD8
T2243	Serdemetan	Apoptosis	Mdm2 inhibitor; p53 activator	HDM2; Mdm2; p53
T6159	LY-2584702 free base	PI3K/Akt/mTOR signaling	mTOR	mTOR (p70 S6K)
T1859	AZD8055	PI3K/Akt/mTOR signaling	mTOR	mTOR
T2706	Palomid 529	PI3K/Akt/mTOR signaling	mTOR inhibitor	mTORC1; mTORC2
T1838	INK 128	PI3K/Akt/mTOR signaling	mTOR inhibitor; PI3K inhibitor	mTOR; mTOR; PI3Kα; PI3Kγ; PI3Kδ
T3153	Serabelisib	PI3K/Akt/mTOR signaling	mTOR inhibitor; PI3K inhibitor	mTOR; p110α; p110β; p110γ; p110δ
T1916	Apitolisib	PI3K/Akt/mTOR signaling	mTOR inhibitor; PI3K inhibitor	mTOR; p110α; p110β; p110γ; p110δ
T2357	GSK1059615	PI3K/Akt/mTOR signaling	mTOR inhibitor; PI3K inhibitor	mTOR; PI3Kα; PI3Kβ; PI3Kγ; PI3Kδ
T1861	Omipalisib	PI3K/Akt/mTOR signaling	mTOR inhibitor; PI3K inhibitor	mTORC1; p110α; p110β; p110γ; p110δ
T2619	CH5132799	PI3K/Akt/mTOR signaling	mTOR inhibitor; PI3K inhibitor	mTOR; PI3Kα; PI3Kβ; PI3Kγ; PI3Kδ
T1970	Gedatolisib	PI3K/Akt/mTOR signaling	mTOR inhibitor; PI3K inhibitor	mTOR; PI3Kα; PI3Kγ
T2265	PI3K-IN-2	Others; PI3K/Akt/mTOR signaling; MAPK	Others inhibitor;S6 Kinase inhibitor;PI3K;mTOR	pPKB; pS6;PI3Kα;PI3Kβ;mTOR;PI3Kγ;PI3Kδ
T1827	Buparlisib	PI3K/Akt/mTOR signaling	PI3K	p110α; p110β; p110γ; p110δ; Vps34
T1994	Pictilisib	PI3K/Akt/mTOR signaling	PI3K	p110α; p110β; p110γ; p110δ
T2672	TG100-115	PI3K/Akt/mTOR signaling	PI3K inhibitor	PI3Kα; PI3Kβ; PI3Kγ; PI3Kδ
T2365	Pilaralisib	PI3K/Akt/mTOR signaling	PI3K inhibitor	PI3Kα; PI3Kβ; PI3Kγ; PI3Kδ
T2073	GSK2636771	PI3K/Akt/mTOR signaling	PI3K inhibitor	PI3Kβ
T6168	ZSTK474	PI3K/Akt/mTOR signaling	PI3K inhibitor	PI3K; PI3Kα; PI3Kβ; PI3Kγ; PI3Kδ
T1988	Duvelisib	PI3K/Akt/mTOR signaling	PI3K inhibitor	PI3Kα; PI3Kβ; PI3Kγ; PI3Kδ
T1999	Taselisib	PI3K/Akt/mTOR signaling; metabolism	PI3K inhibitor; Carbonic Anhydrase	PI3Kα; PI3Kβ; PI3Kγ; PI3Kδ;C2β
T2008	LY294002	PI3K/Akt/mTOR signaling; DNA damage/DNA repair	PI3K; DNA-PK	p110α; p110β; p110δ;DNA-PK
T6250	H 89 2HCl	GPCR/G protein; PI3K/Akt/mTOR signaling; MAPK	PKA; S6 kinase	PKA; S6K1
T3518	GSK269962A	Cell cycle/checkpoint; cytoskeletal signaling; PI3K/Akt/mTOR signaling; stem cells; MAPK	ROCK inhibitor; S6 kinase inhibitor	MSK1; ROCK1; ROCK2; RSK1
TN1712	Gossypin	PI3K/Akt/mTOR signaling; MAPK	S6 kinase	RSK2
T6S1302	Carnosol	PI3K/Akt/mTOR signaling; MAPK	S6 kinase	RSK2
T22422	S6K-18	PI3K/Akt/mTOR signaling; MAPK	S6 kinase	S6K1
T2002	PF4708671	PI3K/Akt/mTOR signaling; MAPK	S6 kinase inhibitor	p70 S6K
T1746	LY-2584702 tosylate	PI3K/Akt/mTOR signaling; MAPK	S6 kinase inhibitor	p70 S6K
T6877	LJH685	PI3K/Akt/mTOR signaling; MAPK	S6 kinase inhibitor	RSK1; RSK2; RSK3
T6878	LJI308	PI3K/Akt/mTOR signaling; MAPK	S6 kinase inhibitor	RSK1; RSK2;RSK3
T4488	GSK25	PI3K/Akt/mTOR signaling; PI3K/Akt/mTOR signaling; MAPK	S6 kinase inhibitor; mTOR inhibitor	RSK1; mTOR (p70 S6K)
T5428	BIX 02565	PI3K/Akt/mTOR signaling; autophagy; MAPK	S6 kinase; LRRK2	RSK2;LRRK2
T2510	Galunisertib	Stem cells	TGF-beta/Smad	TβRI
T1293	Gatifloxacin	DNA damage/DNA repair	Topoisomerase inhibitor	Topo IV
T1878	XAV939	Stem cells; cytoskeletal signaling	Wnt/beta-catenin	TNKS1; TNKS2
T2237	ICG001	Cytoskeletal signaling; stem cells; chromatin/epigenetic	Wnt/beta-catenin inhibitor; Epigenetic Reader Domain	Wnt/β-catenin; CBP
T2436	GSK2801	Chromatin/epigenetic	Epigenetic Reader Domain inhibitor	BAZ2A/2B
T6668	SGC-CBP30	Chromatin/epigenetic	CREBBP/EP300 inhibitor	CREBBP/EP300
T2452	C646	Chromatin/epigenetic	Histone acetyltransferase inhibitor	p300/CBP
T6133	Remodelin	Chromatin/epigenetic	Histone acetyltransferase inhibitor	Acetyltransferase NAT10