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. 2023 Nov 21;4(11):101290. doi: 10.1016/j.xcrm.2023.101290
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

β-Actin (8H10D10) Mouse mAb Cell Signaling Technology Cat #3700; RRID:AB_2242334
p44/42 MAPK (Erk1/2) (3A7) Mouse mAb Cell Signaling Technology #9107; RRID:AB_10695739
Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) Antibody Cell Signaling Technology #9101; RRID:AB_331646
Akt Antibody Cell Signaling Technology #9272; RRID:AB_329827
Phospho-Akt (Thr308) Antibody Cell Signaling Technology #9275; RRID:AB_329828
Stat5 (D2O6Y) Rabbit mAb Cell Signaling Technology #94205; RRID:AB_2737403
Phospho-Stat5 (Tyr694) Antibody Cell Signaling Technology #9351; RRID:AB_2315225
Bcl-2 (124) Mouse mAb Cell Signaling Technology #15071; RRID:AB_2744528
Bcl-xL Antibody Cell Signaling Technology #2762; RRID:AB_10694844
Mcl-1 Antibody Cell Signaling Technology #4572; RRID:AB_2281980
Bim (C34C5) Rabbit mAb Cell Signaling Technology #2933; RRID:AB_1030947
BMF (E5U2J) Rabbit mAb Cell Signaling Technology #50542; RRID:AB_2892182
IRDye® 800CW Goat anti-Rabbit IgG Secondary Antibody LI-COR Biosciences Cat# 925-32211
RRID:AB_2651127
IRDye® 680RD Goat anti-Mouse IgG Secondary Antibody LI-COR Biosciences Cat# 925-68070, RRID:AB_2651128
Bmf Antibody Novus Biologicals Cat# NBP1-76658, RRID:AB_11040482
Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647® Thermo Fisher Scientific Cat# A-21244, RRID:AB_2535812
Alexa Fluor® 647 anti-Cytochrome c Antibody BioLegend Cat# 612310, RRID:AB_2565241
PE anti-mouse CD45 Antibody BioLegend Cat# 103105, RRID:AB_312970
APC/Cyanine7 anti-human CD45 Antibody BioLegend Cat# 304014, RRID:AB_31440
CD45 (Intracellular Domain) (D9M8I) XP® Rabbit mAb Cell Signaling Technology Cat# 13917, RRID:AB_2750898

Bacterial and virus strains

pCW57.1 RRID:Addgene_41393
NEB 10-beta Competent E. coli (High Efficiency) New England Biolabs Cat# C3019I

Biological samples

PDX #1 This paper HM0007
PDX #2 Qin et al.61 CD33-CART-0005
AML patient and healthy donor samples UCSF Hematologic Malignancies Tissue Bank

Chemicals, peptides, and recombinant proteins

RMC-4550 Revolution Medicines ID: 0694550-018
Venetoclax (ABT-199) Selleckchem Cat# S8048; CAS No. 1257044-40-8
Gilteritinib (ASP2215) Selleckchem Cat# S7754; CAS No. 1254053-43-4
WEHI-539 HCl Selleckchem Cat# S7100 CAS No. 2070018-33-4
Trametinib (GSK1120212) Selleckchem Cat# S2673; CAS No. 871700-17-3
S63845 MedChem Express Cat# HY-100741
CAS No. : 1799633-27-4
BIM peptide New England Peptides Cat# LB4609
Alamethicin Enzo Life Sciences Cat BML-A150-0005; CAS No. 27061-78-5
Digitonin Milipore Sigma Cat# D5628; Cas No. CAS Number:
11024-24-1
D-Mannitol Milipore Sigma Cat# M9647; CAS No. 69-65-8
Succinic acid Milipore Sigma Cat# S3674; CAS No. 110-15-6
Ethylenediaminetetraacetic acid Milipore Sigma Cat# E6758; CAS No. 60-00-4
Ethylene glycol-bis(2-aminoethylether)-N,N,N′,N′-tetraacetic acid Milipore Sigma Cat# E3889; CAS No. 67-42-5
HEPES Buffer, N-(2-Hydroxyethyl)piperazineN′-(2-ethanesulfonic acid) Milipore Sigma Cat# SRE0065;
Glycine Thermo Fisher Scientific Cat# BP381-1
CAS No. 56-40-6
Doxycycline Hydrochloride Milipore Sigma Cat# D3072 CAS No. 10592-13-9
Recombinant Human GM-CSF PeproTech Cat# 300-03; Genpept: P04141
Recombinant Human Flt3-Ligand PeproTech Cat# 300-19; Genpept: P49771
Recombinant Human FGF-basic PeproTech Cat# 100-18B; Genpept: P09038
Lipofectamine™ 3000 Thermo Fisher Scientific Cat# L3000008
Lenti-X™ concentrator TakaraBio Cat# 631232
Triton™ X-100 Surfact-Amps™ Detergent Solution Thermo Fisher Scientific Cat# 85111
Paraformaldehyde Aqueous Solution Electron Microscopy Sciences Cat#15710-S
Normal Goat Serum (10%) Thermo Fisher Scientific Cat# 50197Z
ProLong™ Gold Antifade Mountant with DNA Stain DAPI Thermo Fisher Scientific Cat# P36935
D-Luciferin, Potassium Salt Gold Biotechnology Cat# LUCK-100; CAS No. 115144-35-9
Hematoxylin Instant Thermo Fisher Scientific Cat# 6765015

Critical commercial assays

CellTiter-Glo® Luminescent Cell Viability Assay Promega Cat# G7573
Pierce™ BCA Protein Assay Kits Thermo Fisher Scientific Cat# 23225
Ras G-LISA Activation Assay Kit (Colorimetric Based) - 96 Assays Cytoskeleton Cat# BK131
CellEvent™ Caspase-3/7 Green Flow Cytometry Assay Kit Thermo Fisher Scientific Cat# C10427
RNeasy Mini Kit (50) Qiagen Cat# 74104
Discovery Purple Kit Roche Diagnostics Cat# 760229

Deposited data

CRISPR (DepMap Public, Chronos) the Cancer Dependency Map https://depmap.org
RNA-seq data This paper GEO: GSE217359

Experimental models: Cell lines

Molm-14 ATCC RRID:CVCL_7916
MV4-11 ATCC RRID:CVCL_0064
Kasumi-1 ATCC RRID:CVCL_0589
SKNO-1 ATCC RRID:CVCL_2196
OCIAML-3 ATCC RRID:CVCL_1844
NOMO-1 ATCC RRID:CVCL_1609
HL-60 ATCC RRID:CVCL_0002
THP-1 ATCC RRID:CVCL_0006
K562 ATCC RRID:CVCL_0004
HEL ATCC RRID:CVCL_0001
U-937 ATCC RRID:CVCL_0007
HS-5 ATCC RRID:CVCL_3720
LentiX 293T Takara Bio RRID:CVCL_4401
Molm-14 PTPN11 WT-dox This paper N/A
Molm-14 PTPN11 E76K-dox This paper N/A
Molm-14 PTPN11 G60V-dox This paper N/A
Molm-14 PTPN11 S502P-dox This paper N/A
Molm-14 PTPN11 T253M/Q257L-dox This paper N/A
Molm-14 MEK DD-dox This paper N/A
Molm-14 AKT E17K-dox This paper N/A
MV4-11 MEK DD-dox This paper N/A
MV4-11 AKT E17K-dox This paper N/A
Molm-14 BMF KO This paper N/A
SKNO-1 BMF KO This paper N/A
Molm-14 FFLuc This paper N/A
Molm-14 NRAS G12C FFLuc This paper N/A
Kasumi-1 FFLuc This paper N/A
Molm-14 NRAS G12C McMahon et al.14 N/A
Molm-14 NRAS Q61K McMahon et al.14 N/A
Molm-14 FLT3 D835H Smith et al.77 N/A
Molm-14 FLT3 D835V Smith et al.77 N/A
Molm-14 FLT3 D835Y Smith et al.77 N/A
Molm-14 FLT3 N841K Smith et al.77 N/A
Molm-14 FLT3 Y842C Smith et al.77 N/A
Molm-14 FLT3 F691L Smith et al.77 N/A

Experimental models: Organisms/strains

NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ The Jackson Laboratory Strain #:005557
RRID:IMSR_JAX:005557
NOD.Cg-Prkdcscid Il2rgtm1Wjl Tg(CMV-IL3,CSF2,KITLG)1Eav/MloySzJ The Jackson Laboratory Strain #:013062
RRID:IMSR_JAX:013062

Oligonucleotides

Human GAPDH Taqman probe Thermo Fisher Scientific Hs02758991_g1
Human OASL Taqman probe Thermo Fisher Scientific Hs00984387_m1
Human OAS1 Taqman probe Thermo Fisher Scientific Hs00973637_m1
Human IFIT2 Taqman probe Thermo Fisher Scientific Hs01922738_s1
Human BMF Taqman probe Thermo Fisher Scientific Hs00372937_m1
BMF sgRNA guide1: 5’-AAGGCCAGGGCCACAGCAGU-3’ Synthego Custom ID
BMF sgRNA guide2: 5’- AAGCUCCCGGGUUGGGUCAC-3’ Synthego Custom ID
BMF sgRNA guide1: 5’- GGAGCCAUCUCAGUGUGUGG-3’ Synthego Custom ID

Software and algorithms

GraphPad Prism http://www.graphpad.com/ RRID:SCR_002798
FlowJo https://www.flowjo.com/solutions/flowjo RRID:SCR_008520
R Project for Statistical Computing http://www.r-project.org/ RRID:SCR_001905
STAR Dobin et al.78 RRID:SCR_004463
Limma-voom package Law et al.79
ShinyGO http://bioinformatics.sdstate.edu/go/ RRID:SCR_019213
Gene Set Enrichment Analysis Subramanian et al.39 RRID:SCR_003199
NIS Elements RRID:SCR_014329
ImageJ https://imagej.net/ RRID:SCR_003070
SynergyFinder 3.0 Ianevski et al.55
ICE Conant et al.80