|
Antibodies
|
| Snail (C15D3) |
Cell Signaling Technology |
Cat# 3879, RRID: AB_2255011 |
| E-Cadherin (24E10) Rabbit mAb |
Cell Signaling Technology |
Cat# 3195, RRID: AB_2291471 |
| ZEB1 (E2G6Y) |
Cell Signaling Technology |
Cat# 70512 |
| CD44 (E7K2Y) |
Cell Signaling Technology |
Cat# 37259, RRID: AB_2750879 |
| GAPDH (D16H11, HRP conjugate) |
Cell Signaling Technology |
Cat# 8884, RRID: AB_11129865 |
| AAK1 (E8M3P) |
Cell Signaling Technology |
Cat# 61527 |
| RALBP1 (D87H8) |
Cell Signaling Technology |
Cat# 5739, RRID: AB_10697484 |
| Axl (C89E7) Rabbit mAb |
Cell Signaling Technology |
Cat# 8661, RRID: AB_11217435 |
| REPS1 (D6F4) |
Cell Signaling Technology |
Cat# 6404, RRID: AB_11220228 |
| CDK4 (D9G3E) |
Cell Signaling Technology |
Cat# 12790, RRID: AB_2631166 |
| CDK6 (DCS83) |
Cell Signaling Technology |
Cat# 3136, RRID: AB_2229289 |
| CDK2 (78B2) |
Cell Signaling Technology |
Cat# 2546, RRID: AB_2276129 |
| Cyclin D1 (92G2) |
Cell Signaling Technology |
Cat# 2978, RRID: AB_2259616 |
| Cyclin D3 (DCS22) |
Cell Signaling Technology |
Cat# 2936, RRID: AB_2070801 |
| GFP (D5.1) |
Cell Signaling Technology |
Cat# 2956, RRID: AB_1196615 |
| CK2α (polyclonal) |
Novus Biologicals |
Cat# NB100-378, RRID: AB_2230121 |
| CK2β (polyclonal) |
Novus Biologicals |
Cat# NBP1-06515, RRID: AB_1582302 |
|
Bacterial and Virus Strains
|
|
|
|
|
Biological Samples
|
|
|
|
|
|
|
Chemicals, Peptides, and Recombinant Proteins
|
| Kinobead affinity capture reagents |
Laboratory of Dustin J. Maly, University of Washington71
|
Compounds #1, 2, 3, 4, 5, 6 and 7 |
| AZD7762 |
Selleckchem |
Cat#: S1532, CAS#: 860352-01-8 |
| CHIR-124 |
APExBIO |
Cat#: A8394, CAS#: 405168-58-3 |
| GSK-690693 |
MedChemExpress |
Cat#: HY-10249, CAS#: 937174-76-0 |
| Milciclib |
MedChemExpress |
Cat#: HY-10424, CAS#: 802539-81-7 |
| Rebastinib |
MedChemExpress |
Cat#: HY-13024, CAS#: 1020172-07-9 |
| AT9283 |
MedChemExpress |
Cat#: HY-50514, CAS#: 896466-04-9 |
| TAK-901 |
MedChemExpress |
Cat#: HY-12201, CAS#: 934541-31-8 |
| RGB-286638 |
MedChemExpress |
Cat#: HY-15504, CAS#: 784210-87-3 |
| Flavopiridol*HCl |
MedChemExpress |
Cat#: HY-10006, CAS#: 131740-09-5 |
| PF-562271 besylate |
MedChemExpress |
Cat#: HY-10458, CAS#: 939791-38-5 |
| Dabrafenib mesylate |
MedChemExpress |
Cat#: HY-14660A, CAS#: 1195768-06-9 |
| OTSSP167*HCl |
MedChemExpress |
Cat#: HY-15512A, CAS#: 1431698-10-0 |
| CYC-116 |
MedChemExpress |
Cat#: HY-10558, CAS#: 693228-63-6 |
| Silmitasertib |
MedChemExpress |
Cat#: HY-50855, CAS#: 1009820-21-6 |
| SB1317 |
MedChemExpress |
Cat#: HY-15166, CAS#: 937270-47-8 |
| XL228 |
MedChemExpress |
Cat#: HY-15749, CAS#: 898280-07-4 |
| Sapanisertib |
MedChemExpress |
Cat#: HY-13328, CAS#: 1224844-38-5 |
| PF-3758309 |
APExBIO |
Cat#: A3716, CAS#: 898044-15-0 |
| Staurosporine |
LC-Labs |
Cat#: S-9300, CAS#: 62996-74-1 |
| Bosutinib |
Selleckchem |
Cat#: S1014, CAS#: 380843-75-4 |
| Dasatinib |
Selleckchem |
Cat#: S1021, CAS#: 302962-49-8 |
| Linsitinib |
APExBIO |
Cat#: A8334, CAS#: 867160-71-2 |
| LP-935509 |
MedChemExpress |
Cat#: HY-117626, CAS#: 1454555-29-3 |
| Selumetinib (AZD6244) |
Selleckchem |
Cat#: S1008, CAS#: 606143-52-6 |
| Lenvatinib |
Selleckchem |
Cat#: S1164, CAS#: 417716-92-8 |
| Sorafenib |
Selleckchem |
Cat#: S7397, CAS#: 284461-73-0 |
| Regorafenib |
Selleckchem |
Cat#: S1178, CAS#: 755037-03-7 |
| Cabozantinib |
Selleckchem |
Cat#: S1119, CAS#: 849217-68-1 |
| Dinaciclib |
Selleckchem |
Cat#: S2768, CAS#: 779353-01-4 |
| Volasertib (BI 6727) |
Selleckchem |
Cat#: S2235, CAS#: 755038-65-4 |
| Doxorubicin |
Selleckchem |
Cat#: E2516, CAS#: 23214-92-8 |
| Seradigm Fetal Bovine Serum (FBS) |
VWR Life Science |
Cat#: 97068-085 |
| Lysyl Endopeptidase, Mass Spectrometry Grade (Lys-C) |
Wako |
Cat#: 125-05061 |
| Pierce Trypsin Protease, MS Grade |
Thermo Fisher Scientific |
Cat#: 90058 |
| HALT Protease Inhibitor |
Thermo Fisher Scientific |
Cat#: 78430 |
| NuPAGE LDS Sample Buffer |
Thermo Fisher Scientific |
Cat#: NP0007 |
| Bolt 4-12% Bis-Tris Protein Gels |
Thermo Fisher Scientific |
Cat#: NW04120BOX and NW04127BOX |
| TRIzol Reagent |
Thermo Fisher Scientific |
Cat#: 15596026 |
| Phosphatase Inhibitor Cocktail 2 |
Sigma-Aldrich |
Cat#: P5726-5ML |
| Phosphatase Inhibitor Cocktail 3 |
Sigma-Aldrich |
Cat#: P0044-5ML |
| Pierce Protein A Agarose |
Thermo Fisher Scientific |
Cat#: 20333 |
| ReproSil-Pur 120 C18-AQ, 3 µm |
Dr. Maisch |
Cat#: r13.aq. |
|
Critical Commercial Assays
|
| Pierce 660 nm Protein Assay Reagent |
Thermo Fisher Scientific |
Cat#: 22660 |
| RNeasy Mini Kit |
Quiagen |
Cat#: 74104 |
| CellTiter-Glo 2.0 Assay |
Promega |
Cat#: G9241 |
| Clarity Western ECL Substrate |
Bio-Rad |
Cat#: 1705060 |
| Protoscript II First Strand cDNA Synthesis Kit |
New England Biolabs |
Cat#: E6560L |
|
Deposited Data
|
| All MS raw files and MaxQuant output files |
MassIVE Repository of the University of California, San Diego |
Acquisition#: MSV000088067 |
|
Experimental Models: Cell Lines
|
| Human: SNU449, <10 Passages |
ATCC |
Cat#: CRL-2234 |
| Human: HuH-7, <10 Passages |
JRCB Cell Bank |
Cat#: JCRB0403 |
| Human: FOCUS AXL RNAi, <10 Passages |
Laboratory of Taranjit Gujral, Fred Hutchinson Cancer Center, Seattle, WA31
|
N/A |
| Human: FOCUS, <10 Passages |
Laboratory of J. Wands, Brown University72
|
N/A |
| Human: C3A, <10 Passages |
ATCC |
Cat#: CRL-10741 |
| Human: SNU398, <10 Passages |
ATCC |
Cat#: CRL-2233 |
| Human: Hep3B2.1-7, <10 Passages |
ATCC |
Cat#: HB-8064 |
| Human: A-172, <10 Passages |
ATCC |
Cat#: CRL-1620 |
| Human: SNU761, <10 Passages |
Korean Cell Line Bank (KCLB) |
Cat#: 00761 |
| Human: SNU886, <10 Passages |
Korean Cell Line Bank (KCLB) |
Cat#: 00886 |
| Human: HeLa, <10 Passages |
ATCC |
Cat#: CRM-CCL-2 |
| Human: JHH6, <10 Passages |
JRCB Cell Bank |
Cat#: JCRB1030 |
| Human: SH-SY5Y, <10 Passages |
ATCC |
Cat#: CRL-2266 |
| Human: U-2 OS, <10 Passages |
ATCC |
Cat#: HTB-96 |
| Human: SK-N-SH, <10 Passages |
ATCC |
Cat#: HTB-11 |
| Human: JeKo-1, <10 Passages |
ATCC |
Cat#: CRL-3006 |
| Human: Jurkat, <10 Passages |
ATCC |
Cat#: PTS-TIB-152 |
| Human: K562, <10 Passages |
ATCC |
Cat#: CCL-243 |
| Human: SKHep1, <10 Passages |
ATCC |
Cat#: HTB-52 |
| Human: SNU387, <10 Passages |
ATCC |
Cat#: CRL-2237 |
|
Experimental Models: Organisms/Strains
|
|
|
|
| Oligonucleotides |
| AAK1 shRNA#1 |
The RNAi Consortium (TRC) |
TRCN0000001943 |
| AAK1 shRNA#2 |
The RNAi Consortium (TRC) |
Cat#: TRCN0000199939 |
| AAK1 shRNA#3 |
The RNAi Consortium (TRC) |
Cat#: TRCN0000082348 |
| REPS1 shRNA#1 |
The RNAi Consortium (TRC) |
Cat#: TRCN0000053363 |
| REPS1 shRNA#2 |
The RNAi Consortium (TRC) |
Cat#: TRCN0000423162 |
| REPS1 shRNA#3 |
The RNAi Consortium (TRC) |
Cat#: TRCN0000436095 |
| REP2 shRNA#1 |
The RNAi Consortium (TRC) |
Cat#: TRCN0000423057 |
| REP2 shRNA#2 |
The RNAi Consortium (TRC) |
Cat#: TRCN0000428939 |
| REP2 shRNA#3 |
The RNAi Consortium (TRC) |
Cat#: TRCN0000056210 |
| RALBP1 shRNA#1 |
The RNAi Consortium (TRC) |
Cat#: TRCN0000305689 |
| RALBP1 shRNA#2 |
The RNAi Consortium (TRC) |
Cat#: TRCN0000047918 |
| RALBP1 shRNA#3 |
The RNAi Consortium (TRC) |
Cat#: TRCN0000047920 |
|
Recombinant DNA
|
| Lentiviral pLKO.1 Vector Plasmid |
Addgene |
Cat#: 10878 |
| pMD2.G Lentiviral Envelope Plasmid |
Addgene |
Cat#: 12259 |
| pCMVR8.74 Lentiviral Packaging Plasmid |
Addgene |
Cat#: 22036 |
|
Software and Algorithms
|
| MaxQuant/Andromeda, v1.5.2.8 |
https://www.biochem.mpg.de/5111795/maxquant
|
Cox, J. et al.73
|
| Perseus, v1.5.6.0 |
https://www.biochem.mpg.de/5111810/perseus
|
Tayanova, S. et al.74
|
| R-package, gplots v3.0.1, gplots::heatmap.2 |
https://www.rdocumentation.org/packages/gplots/versions/3.0.1
|
N/A |
| R-package, ssGSEA2.0 |
https://github.com/broadinstitute/ssGSEA2.0
|
Krug, K. et al.46
|
| GraphPad Prism, V7 |
https://www.graphpad.com/
|
N/A |
| STRING 11.5, PPI Networks and Enrichment Analysis |
https://string-db.org/
|
Szklarczyk, D. et al.38
|
| BioGRID |
https://thebiogrid.org/
|
Chatr-Aryamontri, A. et al.75
|
| PhosphoSite Plus |
https://www.phosphosite.org/homeAction
|
Hornbeck, P.V. et al.41
|
| BioVenn |
http://www.biovenn.nl/
|
Hulsen, T. et al.76
|
| KinMap |
http://kinhub.org/kinmap/
|
Eid, S. et al.77
|
|
Other
|
| Fluor Chem E Imager |
ProteinSimple/Bio-Techne Brand |
N/A |
| QuantStudio 5 Real-Time PCR System |
Applied Biosystems, Thermo Fisher Scientific |
Cat#: A34322 |
| SpectraMax 190 Multimode Plate Reader |
Molecular Devices |
N/A |
| P-2000 Laser Puller |
Sutter |
N/A |
| EASY-nLC 1200 System |
Thermo Fisher Scientific |
Cat#: LC140 |
| Orbitrap Fusion Lumos Tribrid Mass Spectrometer |
Thermo Fisher Scientific |
Cat#: IQLAAEGAAPFADBMBHQ |
