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. Author manuscript; available in PMC: 2019 Sep 6.
Published in final edited form as: Cell. 2018 Aug 16;174(6):1465–1476.e13. doi: 10.1016/j.cell.2018.07.031
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Mouse anti-L1 Protein of Human Papilloma
Virus clone CAMVIR-1 (RUO)		 BD Biosciences Cat#554171;
RRID:AB_395284
Mouse monoclonal anti-GFP (B-2) Santa Cruz Biotechnology Cat#sc-9996;
RRID:AB_627695
Rabbit polyclonal antibody anti-TGN46 Abcam Cat#ab50595;
RRID:AB_2203289
Rabbit monoclonal anti-VPS35 [EPR11501(B)] Abcam Cat#ab157220; RRID:AB_2636885
Mouse monoclonal anti-VPS35 Abcam Cat#ab57632;
RRID:AB_946126
Rabbit polyclonal anti-L1 J. Schiller, NIH N/A
Mouse antibody 33L1–7 Martin Sapp, LSU N/A
Rabbit monoclonal antibody EEA1 (C45B10) Cell Signaling Technology Cat#3288;
RRID:AB_2096811
Mouse monoclonal anti-GAPDH (6C5) Santa Cruz Biotechnology Cat#sc-32233;
RRID:AB_627679
Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Cat#A-21202;
RRID:AB_141607
Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 Thermo Fisher Cat#A-21206;
RRID:AB_2535792
Bacterial and Virus Strains
One Shot Stbl3 Chemically Competent E. coli Thermo Fisher Cat#C737303
One Shot TOP10 Chemically Competent E. coli Thermo Fisher Cat#C404010
Rosetta 2(DE3) Competent Cells-Novagen Millipore Cat#71397
p16sheLL (Buck et al., 2008) Cat#37320;
Addgene
p5sheLL (Buck et al., 2008) Cat#46953;
Addgene
p16L1-GFP (Buck et al., 2005) Cat#89910;
Addgene
Chemicals, Peptides, and Recombinant Proteins
γ-Secretase Inhibitor XXI, Compound E Millipore Cat#565790;
CAS:209986–17-4
Aphidicolin Santa Cruz Cat#sc-201535;
CAS:38966–21-1
Protein A/G PLUS-Agarose Santa Cruz Cat#sc-2003
Paraformaldehyde Electron Microscopy Sciences Cat#15710;
CAS:30525–89-4
Saponin Sigma Aldrich Cat#47036;
CAS:8047–15-2
Hoechst33324, Trihydrochloride, Trihydrate Thermo Fisher Cat#H3570
Trypan Blue Sigma Aldrich Cat#T6146;
CAS:72–57-1
Puromycin dihydrochloride Sigma Aldrich Cat#P7255;
CAS:58–58-2
OptiPrep Axis-Shield Cat#AXS-1114542
Halt Protease and Phosphatase Inhibitor Single-Use Cocktail, EDTA-Free Thermo Fisher Cat#78443
Alexa Fluor 488 C5 Maleimide Thermo Fisher Cat#A10254
MOPS (morpholinepropanesulfonic acid) AmericanBio Cat#AB01270–00100;
CAS:1132–61-2
Nonidet P-40 Sigma Aldrich Cat#74385;
CAS:9016–45-9
SDS (20%) AmericanBio Cat#AB01922–00500
EDTA, 0.5 M, pH 8.0 AmericanBio Cat#AB00502–01000
Desoxycholic acid sodium salt Sigma Aldrich Cat#D6750;
CAS:302–95-4
Lipofectamine® RNAiMAX Transfection Reagent Thermo Fisher Cat#13778100
Premium Grade TCEP-HCl Thermo Fisher Cat#PG82080
RNase A, DNase and protease-free Thermo Fisher Cat#EN0531
Streptavidin Agarose Thermo Fisher Cat#20349
Glutathione Sepharose GE Healthcare Cat#17075601
His GraviTrap Columns GE Healthcare Cat#45–000-006
Ni-NTA Agarose Qiagen Cat#30210
Phusion High-Fidelity DNA Polymerase New England Biolabs Cat#M0530L
Q5 Site-Directed Mutagenesis Kit New England Biolabs Cat#E0554S
T4 DNA Ligase New England Biolabs Cat#M0202L
PCR Nucleotide Mix Sigma Aldrich Cat# 11581295001
Dulbecco’s Modified Eagle’s Medium - high glucose Sigma Aldrich Cat#D5671
Fetal Bovine Serum Atlanta Biologicals Cat#S11150
L-Glutamine Thermo Fisher Cat#25030081
Pen Strep (Penicillin Streptomycin) Thermo Fisher Cat#15140122
Trypsin-EDTA (0.25%) Thermo Fisher Cat#25200056
Dulbecco’s Phosphate Buffered Saline (DPBS), with
MgCl2 and CaCl2 		Sigma Aldrich Cat#D8662
B-PER™ Bacterial Protein Extraction Reagent Thermo Fisher Cat#78243
Lysozyme Thermo Fisher Cat#90082
DNAse I solution Thermo Fisher Cat#90083
CSPQYTIIADAGDFYLHPSYYMLRKRRKR ABclonal Technology N/A
CSPQYTIIADAGDFYLHPSYYMLAAAAAA ABclonal Technology N/A
CSPQYTIIADAGDFYLHPSYYMLRRR ABclonal Technology N/A
Biotin-SPQYTIIADAGDFYLHPSYYMLRKRRKR ABclonal Technology N/A
Biotin-SPQYTIIADAGDFYLHPSYYMLAAAAAA ABclonal Technology N/A
Biotin-SPQYTIIADAGDFYLHPSYYMLRRR ABclonal Technology N/A
Biotin-SPQYTIIADAGDAAAHPSAAAARKRRKR ABclonal Technology N/A
GFP-L2-WT This paper N/A
GFP-L2–6A This paper N/A
GFP-L2–3R This paper N/A
GFP11–16L2–16CPP This paper N/A
GFP11–16L2-TatCPP This paper N/A
GFP11–16L2–6A This paper N/A
GFP11–16L2–3R This paper N/A
GFP11–16L2–5CPP This paper N/A
GFP11–16L2–18CPP This paper N/A
GFP11–16L2–31CPP This paper N/A
Critical Commercial Assays
Duolink® In Situ PLA Probe Anti-Mouse PLUS Sigma-Aldrich Cat#DUO92001
Duolink® In Situ PLA Probe Anti-Rabbit MINUS Sigma-Aldrich Cat#DUO92005
Duolink® In Situ Detection Reagents Green Sigma-Aldrich Cat#DUO92014
In-Fusion HD cloning Kits Clontech Cat#638909
RNase-Free DNase Set Qiagen Cat#79254
DNeasy Blood and Tissue Kits Qiagen Cat#69504
iQ™SYBR Green Supermix Bio-rad Cat#1708880
BCA Protein Assay Kit Thermo Fisher Cat#23225
Experimental Models: Cell Lines
Human: HaCaT AddexBio
Technologies		 Cat#T0020001
Human: HeLa-sen2 (Goodwin et al., 2000) N/A
Human: HeLa S3 ATCC Cat#CCL-2.2; RRID:CVCL 0058
Human: HaCaT/GFP1–10NES This paper N/A
Human: 293TT (Buck et al., 2005) RRID:CVCL_1D85
Human: HEK293T/17 ATCC Cat#CRL-11268;
RRID:CVCL_1926
Oligonucleotides
siGENOME Human VPS29 siRNA Dharmacon Cat# D-009764–03
siGENOME Human VPS35 siRNA Dharmacon Cat# D-010894–01
siGENOME RISC-Free Control Dharmacon Cat# D-001220–01
HcRed Forward primer: GCACCCAGAGCATGAGAAT This paper N/A
HcRed Reverse primer: TCGTAGGTGGTGGTTCTCT This paper N/A
Recombinant DNA
p16sheLL-CPP-GFP11 This paper N/A
p16sheLL-GFP11-CPP This paper N/A
p16sheLL-3R-GFP11 This paper N/A
p16sheLL-GFP11–3R This paper N/A
p16sheLL.W This paper N/A
p16sheLL.6A This paper N/A
p16sheLL.3R This paper N/A
p16sheLL.4R This paper N/A
p16sheLL.5R This paper N/A
p16sheLL.6R This paper N/A
p16sheLL.7R This paper N/A
p16sheLL.Amphipathic This paper N/A
p16sheLL.Hydrophobic This paper N/A
p5sheLL-CPP-GFP11 This paper N/A
pCAG-HcRed (Matsuda and Cepko, 2004) Cat#11152;
Addgene
pET Biotin His6 GFP LIC cloning vector (H6-msfGFP) Scott Gradia,
UC Berkeley		 Cat#29725;
Addgene
pH6-msfGFP-WT This paper N/A
pH6-msfGFP-6A This paper N/A
pH6-msfGFP-3R This paper N/A
pQlinkG GST-TEV-Vps35 (Harrison et al., 2014) N/A
pET Vps29 (Harrison et al., 2014) N/A
pET Vps26 (Harrison et al., 2014) N/A
pLenti CMV GFP Puro (658–5) (Campeau et al.,
2009)		 Cat#17448;
Addgene
pLentiCMV GFP1–10 This paper N/A
pLentiCMV GFP1–10NES This paper N/A
pCMV-mGFP1–10 (Van Engelenburg and Palmer, 2010) N/A
pCD8-CIMPR (Popa et al., 2015; Seaman, 2007) N/A
pGFP11-CD8-CIMPR This paper N/A
pCD8-CIMPR-GFP11 This paper N/A
pCNX-S1–10(N) (Hyun et al., 2015) N/A
pCNX-S1–10(C) (Hyun et al., 2015) N/A
psPAX2 Didier Trono, EPFL Cat#12260;
Addgene
pMD2.G Didier Trono, EPFL Cat#12259;
Addgene
pGFP11–16L2–16CPP This paper N/A
pGFP11–16L2-TatCPP This paper N/A
pGFP11–16L2–6A This paper N/A
pGFP11–16L2–3R This paper N/A
pGFP11–16L2–5CPP This paper N/A
pGFP11–16L2–18CPP This paper N/A
pGFP11–16L2–31CPP This paper N/A
Software and Algorithms
FlowJo FLOWJO, LLC https://www.flowio.com/solutions/flowjo
RRID:SCR_008520
Fiji National Institutes of Health, USA http://fiii.sc
RRID:SCR_002285
GraphPad Prism GraphPad Software https://www.graphpad.
com/
RRID:SCR_002798
BlobFinder The Centre for Image Analysis at Uppsala University http://www.cb.uu.se/~
amin/BlobFinder/ RRID:SCR_015788
Other
Thinwall Polypropylene Tubes Beckman Coulter Cat#326819
μ-Slide 8 Well ibidi Cat#80826
Slide-A-Lyzer™ Dialysis Cassettes, gamma-irradiated, 10,000 MWCO Thermo Fisher Cat#66453
Slide-A-Lyzer™ G2 Dialysis Cassettes, 2K MWCO, 0.5 mL Thermo Fisher Cat#87717