| Antibodies |
| FITC anti-mouse CD4 antibody (RM4–5) |
Invitrogen |
Cat# 11–0042–85, RRID:AB_464897 |
| APC anti-mouse CD4 antibody (RM4–5) |
Invitrogen |
Cat# 17–0042–81, RRID:AB_469322 |
| APC-eFluor 780 anti-mouse CD4 antibody (RM4–5) |
Invitrogen |
Cat# 47–0042–82, RRID:AB_1272183 |
| Pacific Blue anti-mouse CD8α antibody (5H10) |
Invitrogen |
Cat# MCD0828TR, RRID:AB_2539693 |
| eFIuor 660 anti-mouse CD8α antibody (53–6.7) |
Invitrogen |
Cat# 50–0081–82, RRID:AB_10596646 |
| PE anti-mouse CD25 antibody (PC61) |
BD PharMingen |
Cat# 553866, RRID:AB_395101 |
| PE/Cy5 anti-mouse CD45 antibody (30F-11) |
BioLegend |
Cat# 103110, RRID:AB_312975 |
| FITC anti-mouse CD45 antibody (30F-11) |
BioLegend |
Cat# 103107, RRID:AB_312972 |
| PE/Cy7 anti-mouse CD45 Antibody (30F-11) |
BioLegend |
Cat# 103114, RRID:AB_312979 |
| BV421 rat anti-mouse CD45 (30F-11) |
BD Horizon |
Cat# 563890, RRID:AB_2651151 |
| Biotin anti-mouse CD69 antibody (H1.2F3) |
BD PharMingen |
Cat# 553235, RRID:AB_394724 |
| PE anti-mouse TCRβ antibody (H57) |
BioLegend |
Cat# 109207, RRID:AB_313430 |
| Alexa Fluor 647 anti-mouse TCRβ antibody (H57) |
BioLegend |
Cat# 109218, RRID:AB_493346 |
| FITC anti-mouse TCRγ/δ antibody (GL3) |
BD PharMingen |
Cat# 553177, RRID:AB_394688 |
| PE/Cy7 anti-mouse MHC class I (H-2Kb) antibody (AF6–88.5.5.3) |
Invitrogen |
Cat# 25–5958–82, RRID:AB_2573505 |
| BV786 anti-mouse MHC class I (H-2Kb) antibody (AF6–88.5) |
BD OptiBuild |
Cat# 742863, RRID:AB_2741105 |
| PE anti-mouse CD197 (CCR7) antibody (4B12) |
Invitrogen |
Cat# 12–1971–83, RRID:AB_657689 |
| PE/Cy7 anti-mouse CD326 (EpCAM) antibody (G8.8) |
BioLegend |
Cat# 118216, RRID:AB_1236471 |
| Brilliant Violet 421 anti-mouse CD326 (Ep-CAM) Antibody |
BioLegend |
Cat# 118225, RRID:AB_2563983 |
| Alexa Fluor 647 anti-mouse Ly51 antibody (6C3) |
BioLegend |
Cat# 108312, RRID:AB_2099613 |
| Biotin Ulex europaeus agglutinin I (UEA I) |
Vector Laboratories |
Cat# B-1065, RRID:AB_2336766 |
| DyLight 594 labeled Ulex Europaeus Agglutinin I (UEA I) |
Vector Laboratories |
Cat# DL-1067 |
| Streptavidin Alexa Fluor 546 |
Invitrogen |
Cat# S-11225, RRID:AB_2532130 |
| Streptavidin Alexa Fluor 594 |
Invitrogen |
Cat# S-11227 |
| Streptavidin APC-eFluor 780 |
Invitrogen |
Cat# 47–4317–82, RRID:AB_10366688 |
| Mouse anti-Catenin, beta monoclonal antibody (Clone 14) |
BD Transduction Laboratories |
Cat# 610154, RRID:AB_397555 |
| eFluor 660 anti-mouse Aire antibody (5H12) |
Invitrogen |
Cat# 50–5934–82, RRID:AB_2574257 |
| LC3B (D11) XP Rabbit mAb antibody |
Cell Signaling Technology |
Cat# 3868, RRID:AB_2137707 |
| Mouse anti-Ubiquitin monoclonal antibody (P4D1) |
Cell Signaling Technology |
Cat# 3936, RRID:AB_331292 |
| Rabbit anti-α6 antibody |
Shigeo Murata, University of Tokyo |
N/A |
| Rabbit anti-α7 antibody |
Shigeo Murata, University of Tokyo |
N/A |
| Rabbit anti-β1 antibody |
Shigeo Murata, University of Tokyo |
N/A |
| Rabbit anti-β1i antibody |
Shigeo Murata, University of Tokyo |
N/A |
| Rabbit anti-β2 antibody |
Shigeo Murata, University of Tokyo |
N/A |
| Rabbit anti-β2i antibody |
Shigeo Murata, University of Tokyo |
N/A |
| Rabbit anti-β3 antibody |
Shigeo Murata, University of Tokyo |
N/A |
| Rabbit anti-β5 antibody |
Shigeo Murata, University of Tokyo |
N/A |
| Rabbit anti-β5i antibody |
Shigeo Murata, University of Tokyo |
N/A |
| Rabbit anti-β5t antibody |
Murata et al., 2007 |
N/A |
| Rabbit anti-mouse β5t polyclonal antibody |
MBL International Corporation |
Cat# PD021, RRID:AB_2171885 |
| Rabbit anti-Rpn1 antibody |
Shigeo Murata, University of Tokyo |
N/A |
| Rat anti-Rpn13 antibody |
Shigeo Murata, University of Tokyo |
N/A |
| Rabbit anti-beta-Actin antibody (13E5) |
Cell Signaling Technology |
Cat# 4970, RRID:AB_2223172 |
| Alexa Fluor Plus 488 goat anti-mouse IgG (H+L) highly cross-adsorbed secondary antibody |
Invitrogen |
Cat# A32723, RRID:AB_2633275 |
| Donkey anti-rabbit IgG (H+L) antibody- Alexa Fluor 488 |
Invitrogen |
Cat# A-21206, RRID:AB_2535792 |
| Goat anti-rabbit IgG (H+L) antibody, Alexa Fluor 488 highly cross-adsorbed secondary antibody |
Invitrogen |
Cat# A-11034, RRID:AB_ 2576217 |
| Sheep anti-mouse IgG ECL antibody, HRP conjugated |
GE Healthcare |
Cat# NA9310–1ml, RRID:AB_772193 |
| Donkey anti-rabbit IgG ECL antibody, HRP conjugated |
GE Healthcare |
Cat# NA9340–1ml, RRID:AB_772191 |
| Goat anti-rat IgG, whole Ab ECL antibody, HRP conjugated |
GE Healthcare |
Cat# NA935, RRID:AB_772207 |
| Chemicals, Peptides, and Recombinant Proteins |
| Liberase TM Research Grade |
Roche |
Cat# 5401127001 |
| DNase I recombinant, RNase-free |
Roche |
Cat# 04716728001 |
| CD45 MicroBeads, mouse |
Miltenyi Biotec |
Cat# 130–052–301 |
| Me4BodipyFL-Ahx3Leu3VS (Proteasome activity probe) |
BostonBiochem |
Cat# I-190 |
| MG132 (Proteasome inhibitor) |
AdooQ Bioscience |
Cat# A11043 |
| MG-132, ≥ 95% by HPLC |
Millipore |
Cat# 474787 |
| Brefeldin A |
Sigma Aldrich |
Cat# B5936 |
| Critical Commercial Assays |
| Cell Trace Violet Cell Proliferation Kit |
Thermo Fisher Scientific |
Cat# C34557
|
| His Bind Purification Kit |
Novagen |
Cat# 70239 |
| RNeasy Plus Micro Kit |
QIAGEN |
Cat# 74034 |
| SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing |
Clontech |
Cat# 634888 |
| Nextera XT DNA Library Preparation Kit |
Illumina |
Cat# FC-131–1024 |
| RapiGest SF Surfactant |
Waters |
Cat# 186001861 |
| Trypsin/Lys-C Mix, Mass Spec Grade |
Promega |
Cat# V5072 |
| Pierce Quantitative Colorimetric Peptide Assay |
Thermo Fisher Scientific |
Cat# 23275 |
| TMT10plex Isobaric Label Reagent Set |
Thermo Fisher Scientific |
Cat# 90309 |
| Pierce High pH Reversed-Phase Peptide Fractionation Kit |
Thermo Fisher Scientific |
Cat# 84868 |
| Deposited Data |
| RNA sequencing data |
The DNA Data Bank of Japan |
DRA008167, DRA008878 |
| MS proteomics data |
jPOST partner repository |
PXD013132, PXD013133 |
| Experimental Models: Cell Lines |
| NIH 3T3 |
ATCC |
Cat# CRL-1658, RRID:CVCL_0594 |
| Experimental Models: Organisms/Strains |
| Mouse: C57BL/6N |
SLC Japan |
N/A |
| Mouse: C57BL/6J |
The Jackson Laboratory |
RRID:IMSR_JAX:000664 |
| Mouse: BALB/cJ |
The Jackson Laboratory |
RRID:IMSR_JAX:000651 |
| Mouse: DBA/2J |
The Jackson Laboratory |
RRID:IMSR_JAX:000671 |
| Mouse: Keratin 5 promoter-driven Cyclin D1 Tg |
Robles et al., 1996 |
N/A |
| Mouse: β5t−/− (β5t Venus/Venus) |
Murata et al., 2007 |
N/A |
| Mouse: β5t−/− (β5t Cre/Cre) |
Ohigashi et al., 2013 |
N/A |
| Mouse: β5i−/−
|
Fehling et al., 1994 |
N/A |
| Recombinant DNA |
| pET28a-β5 |
Shigeo Murata, University of Tokyo |
N/A |
| pET28a-β5i |
Shigeo Murata, University of Tokyo |
N/A |
| pET28a-β5t |
Shigeo Murata, University of Tokyo |
N/A |
| Software and Algorithms |
| GraphPad Prism |
GraphPad Software |
RRID:SCR_002798 |
| FlowJo |
FlowJo |
RRID:SCR_008520 |
| ImageJ |
NIH |
RRID:SCR_003070 |
| CLC Genomics Workbench |
QIAGEN |
RRID:SCR_011853 |
| DAVID |
Leidos Biomedical Research, Inc |
RRID:SCR_001881 |
| Proteome Discoverer |
Thermo Fisher Scientific |
RRID:SCR_014477 |
| Adobe Photoshop |
Adobe |
RRID:SCR_014199 |
