Table 2 Key resources table.

From: Atypical cellular responses mediated by intracellular constitutive active TrkB (NTRK2) kinase domains and a solely intracellular NTRK2-fusion oncogene

Reagent or Resource

Source

Identifier

Primary antibodies – dilution from stock

Rabbit monoclonal anti-panTrk (C-term) – A7H6R (1:500 – 1:10,000) (anti-panTrk)

Cell Signaling

Cat# 92991;

RRID: AB_2800196

Rabbit monoclonal anti-SQSTM1/p62 (D5E2) (1:1000)

Cell Signaling

Cat# 8025

RRID: AB_10859911

Rabbit monoclonal anti-pY490-TrkA (anti-pY516-TrkB) C35G9 – Shc site (1:500) (anti-pTrk-shc)

Cell Signaling

Cat# 4619;

RRID: AB_10235585

Rabbit monoclonal anti-pY674/675-TrkA (anti-pY706/707–TrkB) C50F3 (1:500) (anti-pTrk-kin)

Cell Signaling

Cat# 4621;

RRID: AB_916186

Rabbit monoclonal anti-pY785-TrkA (anti-pY816-TrkB) C67C8 – PLCγ site (1:500) (anti-pTrk-PLCγ)

Cell Signaling

Cat# 4168;

RRID: AB_10620952

Goat polyclonal anti-TrkB (receptor domain) (1:1000) (anti-TrkB)

R&D Systems

Cat# AF1494;

RRID: AB_2155264

Rabbit polyclonal anti-FAK (1:500)

Cell Signaling

Cat# 3285;

RRID: AB_2269034

Rabbit polyclonal anti- pY397-FAK (1:500)

Cell Signaling

Cat# 3283;

RRID: AB_2173659

Rabbit polyclonal anti-pY576/577-FAK (1:500)

Cell Signaling

Cat# 3281;

RRID: AB_331079

Rabbit polyclonal anti- pY925-FAK (1:500)

Cell Signaling

Cat# 3284;

RRID: AB_10831810

Rabbit monoclonal anti-44/42-MAP Kinase 137F5 (1:1000)

Cell Signaling

Cat# 4695;

RRID: AB_390779

Rabbit monoclonal anti-p44/42-MAP Kinase (D13.14.4E) (1:1000)

Cell Signaling

Cat# 4370;

RRID: AB_2315112

Rabbit polyclonal anti-Cofilin (1:1000)

Cell Signaling

Cat# 3312;

RRID: AB_330235

Rabbit monoclonal anti-pS3-Cofilin 77G2 (1:1000)

Cell Signaling

Cat# 3313;

RRID: AB_2080597

Mouse monoclonal anti-Nestin (human) 10C2 (1:1000) (Western)

Merck Millipore

Cat# MAB5326;

RRID: AB_2251134

Mouse monoclonal anti-hNestin (1:2400) (IHC)

R&D Systems

Cat# MAB1259;

RRID: AB_2251304

Mouse monoclonal anti-γ-Adaptin (1:1000)

BD Biosciences

Cat# 610385;

RRID: AB_397768

Mouse monoclonal anti-HA.11 Clone 16B12

Covance

Cat# MMS-101P;

RRID: AB_10064068

Rabbit monoclonal anti SQSTM1/p62 (D5E2)

Cell Signaling

Cat# 8025;

RRID:AB_10859911

Secondary antibodies (all stored as 0.5 mg/ml)

Donkey anti goat IgG affiniPure (H + L)-Alexa488 (1:800)

Jackson

Cat# 705-545-147;

RRID: AB_2336933

Donkey anti goat affiniPure-Alexa647

Jackson

Cat# 705-605-003;

RRID: AB_2340436

Donkey anti goat HRP IgG (H + L) (1:5000)

Jackson

Cat# 705-035-147;

RRID: AB_2313587

Donkey anti rabbit IgG affiniPure (H + L)-Cy3-550 (1:800)

Jackson

Cat# 711-165-152;

RRID: AB_2307443

Peroxidase AffiniPure Goat Anti-Rabbit IgG (H + L) (1:5000)

Jackson

Cat# 111-035-144;

RRID: AB_2307391

Goat anti mouse IgG affiniPure (H + L)-Alexa488 (1:800)

Invitrogen

Cat# A11029;

RRID: AB_138404

Peroxidase AffiniPure Goat Anti-Mouse IgG (H + L) (1:5000)

Jackson

Cat# 115-035-146;

RRID: AB_2307392

Goat Anti-Mouse IgG1 affiniPure, Cy3-conjugated, Fc_Subclass 1-specific (human glioblastoma tissue)

Jackson

Cat# 115-165-205;

RRID: AB_2338694

FACS: R-Phycoerythrin AffiniPure Goat Anti-Mouse IgG, Fcγ subclass 2a specific

Jackson

Cat# 115-115-206

RRID: AB_2338621

Chemicals, Peptides and Recombinant Proteins

Acti-stain-670-Phalloidin

Cytoskeleton

Cat# PHDN1

Ammonium persulfate (APS)

Sigma–Aldrich

Cat# A3678

Ampicillin

Roth

Cat# K029

Aquapolymount

Polyscienes Inc.

Cat# 18606

Blotting Grade Blocker – non-fat dry milk

BioRad

Cat# 1706404

β-mercaptoethanol

Sigma

Cat# M7154

BSA (Bovine Serum Albumin)

Sigma–Aldrich

Cat# A7030

BDNF (brain-derived neurotrophic factor) – with carrier

R&D Systems

Cat# 248-BDB

Bromophenol blue

Sigma

Cat# B-8026

CheLuminate-HRP PicoDetect

Applichem

Cat# A3417,1200

cOmplete Tablets mini EDTA-free

Roche

Cat# 4693159001

DAPI - (4’,6-diamidino-2-phenylindol)

Sigma–Aldrich

Cat# D9542

DMEM (1×) + GlutaMAX

Gibco

Cat# 61965-026

Opti-MEM + GlutaMAX

Gibco

Cat# 51985-034

DMSO (Dimethylsulfoxide)

Roth

Cat# 4720

Doxycycline

Sigma–Aldrich

Cat# D9891-1G

ECL Prime

GE Healthcare

Cat# RPN2232

Entrectinib (RXDX-101)

Selleckchem

Cat# S7998

Fetal calf serum (FCS)

Linaris

Cat# AB-6000

Gene Ruler - 1 kb DNA ladder

Fermentas

Cat# SM0311

Gene Ruler - 100 bp DNA ladder

Thermo Scientific

Cat# SM0241

Hank’s Balanced Salt Solution (HBSS)

Gibco

Cat# 14170

HD Green Plus DNA stain

Intas

Cat# ISII-HDGreen Plus

HEPES

Sigma

Cat# H4034-25G

Immobilon Western HRP substrate

Merck Milipore

Cat# P90720

Immun-Blot PVDF Membrane

BioRad

Cat# 1620177

K252a

Abcam

Cat# ab120419

Larotrectinib (LOXO-101) sulfate

Selleckchem

Cat# S7960

Lipofectamine 2000

Invitrogen

Cat# 11668-019

Luminaris HiGreen qPCR Master Mix

Thermo Fisher Scientific

Cat# K0992

4–15% Mini-PROTEAN® TGX™ Precast Protein Gels, 10-well, 30 µl

BioRad

Cat# 4561083 S

Nonidet P40 Substitute

Sigma

Cat# 74385

Paraformaldehyde

Merck

Cat# A113 13

Penicillin-Streptomycin (5000 U/mL)

Gibco

Cat# 15070-063

Puromycin

InvivoGen

Cat# ant-pr-1

Polyacrylamide 30%

BioRad

Cat# 1610158

Poly-D,L-ornithine hydrobromide (PORN)

Sigma

Cat# P8638

Poly-L Lysine hydrobromide (PLL)

Sigma

Cat# P2636

Prestained protein ladder

Thermo Scientific

Cat# 26616

SDS (Sodiumdodecylsulfate)

Applichem

Cat# A2572,1000

Superscript III RT

Invitrogen

Cat# 18080

TEMED (N,N,N′,N′-Tetramethylethylenediamine)

Merck

Cat# UN2372

Tris base

Roth

Cat# 4855.3

Tris HCl

Roth

Cat# 6771.1

Triton X100

Sigma–Aldrich

Cat# 9002-93-1

TrypLE-Express

Gibco

Cat# 12605-010

Tween 20

Sigma

Cat# P1379

Experimental models: Cell lines

HEK293

ATCC

Cat# 305

U87MG

ATCC

Cat# HTB-14

NIH-3T3

Cell Lines Services

Cat# 400101

Critical commercial assays

Pierce BCA Protein Assay Kit

Thermo Scientific

Cat# 23225

NucleoBond Xtra Midi EF

Macherey Nagel

Cat# 740420

Monarch-PCR & DNA Cleanup Kit

New England Biolabs

Cat# T1030S

Monarch-DNA Gel Extraction Kit

New England Biolabs

Cat# T1020S

RNeasy Mini Kit

Qiagen

Cat# 74104

Quick Blunting Kit

New England Biolabs

Cat# E1201

Quick Change II XL - Site directed mutagenesis Kit

Agilent Technologies

Cat# 200521

Agilent RNA 6000 Nano Kit

Agilent Technologies

Cat# 5067-1511

TruSeq Stranded mRNA Library Prep

Illumina

Cat# 20020595

Agilent DNA 1000 Kit

Agilent Technologies

Cat# 5067-1504

Software and algorithms

ImageJ

https://imagej.nih.gov/ij/

RRID:SCR_003070

Adobe Photoshop CS5 Extended

http://www.adobe.com/

RRID:SCR_014199

OriginPro

https://www.originlab.com/

RRID:SCR_014212

GraphPad Prism

http://www.graphpad.com/

RRID:SCR_002798

Olympus Fluoview – FV10-ASW 3.0

http://www.olympus-lifescience.com/en/

RRID:SCR_014215

Leica LAS AF Image Acquisition Software

http://www.leica-microsystems.com/

RRID:SCR_013673

LightCycler Roche

http://www.roche-applied-science.com/

RRID:SCR_012155

Python Programming Language

https://www.python.org/

RRID:SCR_008394

FACS: Attune Nxt Nxt analysis software

https://www.thermofisher.com/us/en/home/life-science/cell-analysis/flow-cytometry/flow-cytometers/attune-acoustic-focusing-flow-cytometer.html

RRID:SCR_019590

Illumina NextSeq RTA 550 System (v3.7.17)

https://www.illumina.com/systems/sequencing-platforms/nextseq.html

RRID:SCR_016381

bcl2fastq2 - Illumina (v2.20.0.422)

https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html

RRID:SCR_015058

Cutadapt (v2.5)

(Martin 2011)

RRID:SCR_011841

STAR (v2.7.2b)

(Dobin et al., 2013)

RRID:SCR_004463

featureCounts (v1.6.4)

(Liao et al.,2014) http://bioinf.wehi.edu.au/featureCounts/

RRID:SCR_012919

DESeq2 (v1.24.0)

(Love et al., 2014) https://bioconductor.org/packages/release/bioc/html/DESeq2.html

RRID:SCR_015687

g:Profiler

http://biit.cs.ut.ee/gprofiler/

RRID:SCR_006809

Reactome

https://reactome.org/

RRID:SCR_003485

Back to article page