KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| PE-Cy7 Rat Anti-Mouse CD45R/B220 | BD Biosciences | Clone RA3-6B2; Cat#561881; RRID:AB_10893024 |
| BUV737 Rat Anti-Mouse CD45R/B220 | BD Biosciences | Clone RA3-6B2; Cat#564449; RRID:AB_2738813 |
| APC Rat Anti-Mouse CD45R/B220 | BD Biosciences | Clone RA3-6B2; Cat#553092; RRID:AB_398531 |
| PE Rat Anti-Mouse CD19 | BD Biosciences | Clone 1D3; Cat#557399; RRID:AB_396682 |
| BV786 Rat Anti-Mouse CD19 | BD Biosciences | Clone 1D3; Cat#563333; RRID:AB_2738141 |
| PE Rat Anti-Mouse T- and B Cell Activation Antigen | BD Biosciences | Clone GL7; Cat#561530; RRID:AB_10715834 |
| FITC Hamster Anti-Mouse CD95 | BD Biosciences | Clone Jo2; Cat#561979; RRID:AB_10892808 |
| BV421 Rat Anti-Mouse CD138 | BD Biosciences | Clone 281-2; Cat#562610; RRID:AB_11153126 |
| CD38 Monoclonal Antibody, Alexa Fluor 700 | Thermo Fisher Scientific | Clone 90; Cat#56-0381-82; RRID:AB_657740 |
| CD184 (CXCR4) Monoclonal Antibody, PE | Thermo Fisher Scientific | Clone 2B11; Cat#12-9991-82; RRID:AB_891391 |
| PE-Cy7 Rat Anti-Mouse CD86 | BD Biosciences | Clone GL1; Cat#560582; RRID:AB_1727518 |
| CD4 Monoclonal Antibody, FITC | Thermo Fisher Scientific | Clone GK1.5; Cat#11-0041-81; RRID:AB_464891 |
| PE-Cy7 Rat Anti-CD11b | BD Biosciences | Clone M1/70; Cat#561098; RRID:AB_2033994 |
| F4/80 Monoclonal Antibody, APC-eFluor 780 | Thermo Fisher Scientific | Clone BM8; Cat#47-4801-80; RRID:AB_2637188 |
| BUV395 Hamster Anti-Mouse CD3e | BD Biosciences | Clone 145-2C11; Cat#563565; RRID:AB_2738278 |
| PE Anti-Mouse NK1.1 (CD161) | Tonbo Biosciences | Clone PK136; Cat#50-5941; RRID:AB_2621804 |
| FITC Anti-Mouse MHC Class II (I-A/I-E) | Tonbo Biosciences | Clone M5/114.15.2; Cat#35-5321; RRID:AB_2621715 |
| APC Anti-Mouse CD11c | Tonbo Biosciences | Clone N418; Cat#20-0114; RRID:AB_2621557 |
| PerCP-Cyanine5.5 Anti-Mouse Ly-6G | Tonbo Biosciences | Clone 1A8; Cat#65-1276; RRID:AB_2621899 |
| Alexa Fluor700 anti-mouse Ly-6C Antibody | Biolegend | Clone HK1.4; Cat#128024; RRID:AB_10643270 |
| PerCP-Cy5.5 Mouse Lineage Antibody Cocktail | BD Biosciences | Cat#561317; RRID:AB_10612020 |
| APC/Cyanine7 anti-mouse CD117 (c-kit) Antibody | Biolegend | Clone 2B8; Cat#105826; RRID:AB_1626278 |
| Pacific Blue anti-mouse Ly-6A/E (Sca-1) Antibody | Biolegend | Clone E13-161.7; Cat#122520; RRID:AB_2143237 |
| APC anti-mouse CD150 (SLAM) Antibody | Biolegend | Clone TC15-12F12.2; Cat#115910; RRID:AB_493460 |
| PE Hamster Anti-Mouse CD48 | BD Biosciences | Clone HM48.1; Cat#557485; RRID:AB_396725 |
| BUV737 Rat Anti-Mouse CD127 | BD Biosciences | Clone SB/199; Cat#612841; RRID:AB_2870163 |
| CD34 Monoclonal Antibody, FITC | Thermo Fisher Scientific | Clone RAM34; Cat#11-0341-82; RRID:AB_465021 |
| PE-Cy7 Rat Anti-Mouse CD16/CD32 | BD Biosciences | Clone 2.4G2; Cat#560829; RRID:AB_10563207 |
| Phospho-S6 Ribosomal Protein (Ser235/236) Rabbit mAb (Alexa Fluor® 647 Conjugate) | Cell Signaling Technology | Clone D57.2.2E; Cat#4851; RRID:AB_10695457 |
| APC Rat anti-Mouse IgG1 | BD Biosciences | Clone A85-1; Cat#560089; RRID:AB_1645625 |
| CD45.1 Monoclonal Antibody, PerCP-Cyanine5.5 | Thermo Fisher Scientific | Clone A20; Cat#45-0453-82; RRID:AB_1107003 |
| CD45.2 Monoclonal Antibody, APC | Thermo Fisher Scientific | Clone 104; Cat#17-0454-81; RRID:AB_469399 |
| APC/Cyanine7 anti-mouse CD45.2 Antibody | Biolegend | Clone 104; Cat#109824; RRID:AB_830789 |
| Biotin Rat Anti-Mouse CD185 (CXCR5) | BD Biosciences | Clone 2G8; Cat#551960; RRID:AB_394301 |
| PE Streptavidin-Phycoerythrin antibody | BD Biosciences | Cat#554061; RRID:AB_10053328 |
| CD279 (PD-1) Monoclonal Antibody, PE-Cyanine7 | Thermo Fisher Scientific | Clone J43; Cat#25-9985-80; RRID:AB_10853672 |
| Phospho-p70 S6 Kinase (Thr389) Rabbit mAb | Cell Signaling Technology | Clone 108D2; Cat#9234; RRID:AB_2269803 |
| p70 S6 Kinase Rabbit mAb | Cell Signaling Technology | Clone 49D7; Cat#2708; RRID:AB_390722 |
| CD4 Monoclonal Antibody, FITC | Thermo Fisher Scientific | Clone GK1.5; Cat#11-0041-81; RRID:AB_464891 |
| BUV395 Rat Anti-Mouse CD4 | BD Biosciences | Clone GK1.5; Cat#563790; RRID:AB_2738426 |
| APC-Cyanine7 Anti-Human/Mouse CD44 | Tonbo Biosciences | Clone IM7; Cat#25-0441; RRID:AB_2621628 |
| PE Rat Anti-Mouse CD62L | BD Biosciences | Clone MEL-14; Cat#553151; RRID:AB_394666 |
| PE-Cy7 Hamster Anti-Mouse CD69 | BD Biosciences | Clone H1.2F3; Cat#552879 |
| PerCP-Cy5.5 Rat Anti-Mouse CD25 . | BD Biosciences | Clone PC61; Cat#551071; RRID:AB_394031 |
| Mouse CD40/TNFRSF5 Antibody | R&D Systems | Cat#MAB440; RRID:AB_358378 |
| In Vivo Ready Anti-Mouse CD3e | Tonbo Biosciences | clone 145-2C11; Cat#40-0031; RRID:AB_2621436 |
| In Vivo Ready Anti-Mouse CD28 | Tonbo Biosciences | clone 37.51; Cat#40-0281; RRID:AB_2621445 |
| Rabbit anti-TFEB Antibody | Bethyl Lab. | Cat#A303-673A; RRID:AB_11204751 |
| Chemicals, peptides, and recombinant proteins | ||
| Live/Dead AQUA dead cell stain | Life Technologies | Cat#L34957 |
| Sheep Red Blood Cells | Oxoid | Cat#SR0053B |
| CD43 (Ly-48) MicroBeads, mouse | Miltenyi Biotec | Cat#130-049-801; RRID:AB_2861373 |
| RPMI-1640 Medium | Sigma-Aldrich | Cat#R8758 |
| HyClone Fetal Bovine Serum | Hyclone | SV30160.03 |
| β-mercaptoethanol | GIBCO | Cat#31350-010 |
| HEPES | Lonza | Cat#BE17-737E |
| Penicillin/Streptomycin (5.000 U/ml) | GIBCO | Cat#15070-063 |
| Recombinant Mouse IL-4 Protein | R&D Systems | Cat#404-ML |
| CellTrace CFSE Cell Proliferation Kit, for flow cytometry | Life Technologies | Cat#C34554 |
| Erythrocyte Lysis Buffer (Buffer EL) | QIAGEN | Cat#79217 |
| Fixation/Permeabilization Solution Kit | BD Biosciences | Cat#554714; RRID:AB_2869008 |
| Click-iT® Plus EdU Alexa Fluor® 647 Flow Cytometry Assay Kit | Life Technologies | Cat#C10634 |
| TRIzol Reagent | Invitrogen | Cat#15596026 |
| RNase-Free DNase Set. | QIAGEN | Cat#79254 |
| SuperScript IV VILO Master Mix | Invitrogen | Cat#11756500 |
| GoTaq® qPCR Master Mix | Promega | Cat#6001 |
| Arcturus PicoPure RNA Isolation kit | Applied Biosystems | Cat#12204-01 |
| CD4+ T Cell Isolation Kit, mouse | Miltenyi Biotec | Cat#130-104-454 |
| CD45R (B220) MicroBeads, mouse | Miltenyi Biotec | Cat#130-049-501 |
| Collagen, Type I solution | Sigma-Aldrich | Cat#C3867 |
| Dulbecco’s MEM (DMEM) F-12 w/o Amino Acids | US Biological Life Science | Cat#D9801-10 |
| Sodium hydrogen carbonate (NaHCO3) | Sigma-Aldrich | Cat#1063291000 |
| D-(+)-Glucose solution | Sigma-Aldrich | Cat#G8769 |
| Critical commercial assays | ||
| Mouse IgM ELISA kit | Abcam | Cat#ab133047 |
| Mouse IgG1 ELISA Kit | Abcam | Cat#ab133045 |
| Deposited data | ||
| RNaseq from RagCQ119L/+ GC B cells | This paper | GEO: GSE174003 |
| RNaseq from VavPBcl2/RagCQ119L/+ lymphomas | This paper | GEO: GSE173619 |
| Gene expression profiling in RagC Q119L murine germinal center B cells and B220+ lymphoma cells | This paper | GEO: GSE174004 |
| Experimental models: Cell lines | ||
| primary B cells | RagCQ119L mice | N/A |
| primary T cells | RagCQ119L mice | N/A |
| primary MEFs | RagCQ119L mice | N/A |
| primary hepatocyes | RagCQ119L mice | N/A |
| Experimental models: Organisms/strains | ||
| RragcQ119L/+ | This Paper | N/A |
| B6.129S2-Ighmtm1Cgn/J (IghmμMT) | The Jackson Laboratory | Cat#002288 |
| VavP-Bcl2 | Susanne Cory lab; Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia | N/A |
| Oligonucleotides | ||
| Il-6-FW: TACCCCGATTCAGGTGAT. | Ortega-Molina et al., 2015 | N/A |
| Il-6-RV: TTGAGCAGAAGAGCTGCTACGT. | Ortega-Molina et al., 2015 | N/A |
| p21-FW: GTGGGTCTGACTCCAGCCC. | Lopez-Guadamillas et al., 2016 | N/A |
| p21-RV: CCTTCTCGTGAGACGCTTAC | Lopez-Guadamillas et al., 2016 | N/A |
| p16-FW: TACCCCGATTCAGGTGAT. | Lopez-Guadamillas et al., 2016 | N/A |
| p16-RV: TTGAGCAGAAGAGCTGCTACGT | Lopez-Guadamillas et al., 2016 | N/A |
| Il-1b-FW: TCTTTGAAGTTGACGGACCC. | This paper | N/A |
| Il-1b-RV: TCCACGGGAAAGACACAGGT | This paper | N/A |
| Ccl2-FW: GGTCCCTGTCATGCTTCTGG | This paper | N/A |
| Ccl2-RV: GAGTAGCAGCAGGTGAGTGG. | This paper | N/A |
| Cxcl1-FW: CGCCTATCGCCAATGAGCT. | This paper | N/A |
| Cxcl1-RV: ATGACTTCGGTTTGGGTGCA | This paper | N/A |
| Cxcl2-FW: GTGAACTGCGCTGTCAATGC. | This paper | N/A |
| Cxcl2-RV: ACTTCTGTCTGGGCGCAG. | This paper | N/A |
| Timp1-FW: CTTCTGCAACTCGGACCTGG. | This paper | N/A |
| Timp1-RV: CGCTGGTATAAGGTGGTCTCG | This paper | N/A |
| Mmp3-FW: GACTCAAGGGTGGATGCTGT. | De Cecco et al., 2019 | N/A |
| Mmp3-RV: CCAACTGCGAAGATCCACTG | De Cecco et al., 2019 | N/A |
| Actin-FW: GGCACCACACCTTCTACAATG. | Ortega-Molina et al., 2015 | N/A |
| Actin-RV: GTGGTGGTGAAGCTGTAGCC | Ortega-Molina et al., 2015 | N/A |
| Software and algorithms | ||
| Prism 9 (version 9.1.0) | GraphPad | https://www.graphpad.com |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| FACS DIVA | BD Biosciences | N/A |
| GSEA software | Subramanian et al., 2005 | http://www.gsea-msigdb.org/gsea/index.jsp |
| Nextpresso pipeline | Graña et al., 2017 | http://ubio.bioinfo.cnio.es/people/ograna/nextpresso/. |
| TopHat2 | Trapnell et al., 2012 | https://ccb.jhu.edu/software/tophat/index.shtml |
| SAMTOOLS v.1.9 | Li et al., 2009 | http://samtools.sourceforge.net/ |
| Bowtie | Langmead et al., 2009 | http://bowtie-bio.sourceforge.net/index.shtml |
| HTSeq | Anders et al., 2015 | https://www-huber.embl.de/HTSeq |
| DESeq2 | Love et al., 2014 | http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. |
| FlowJo | TreeStar | https://www.flowjo.com |
| Other | ||
| Flow Cytometry Gating strategy | This paper | Data S1 |
| Uncropped western blots | This paper | Data S2 |