KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| APC Anti-mouse CD3ε (17A2) | BioLegend | Cat #100236; RRID:AB_2561456 |
| FITC Anti-mouse CD3ε (17A2) | BioLegend | Cat #100204; RRID:AB_312661 |
| PE Anti-mouse CD3ε (17A2) | BioLegend | Cat #100206; RRID:AB_312663 |
| Brilliant Violet 650 Anti-mouse CD3ε (17A2) | BioLegend | Cat #100229 RRID: AB_11204249 |
| APC Anti-mouse CD4 (GK1.5) | BioLegend | Cat #100412; RRID:AB_312697 |
| FITC Anti-mouse CD4 (GK1.5) | BioLegend | Cat #100406; RRID:AB_312691 |
| PE Anti-mouse CD4 (GK1.5) | BioLegend | Cat #100408; RRID:AB_312693 |
| APC Anti-mouse CD5 (53–7.3) | BioLegend | Cat #100626; RRID:AB_2563929 |
| FITC Anti-mouse CD5 (53–7.3) | BioLegend | Cat #100606; RRID:AB_312735 |
| PE Anti-mouse CD5 (53–7.3) | BioLegend | Cat #100608; RRID:AB_312737 |
| APC Anti-mouse CD8α (53–6.7) | eBioscience | Cat #17–0081-82; RRID:AB_469335 |
| FITC Anti-mouse CD8α (53–6.7) | eBioscience | Cat #11–0081-85; RRID:AB_464916 |
| PE Anti-mouse CD8α (53–6.7) | eBioscience | Cat #12–0081-83; RRID:AB_465531 |
| APC Anti-mouse CD11b (M1/70) | eBioscience | Cat #17–0112-82; RRID:AB_469343 |
| APC efluor780 Anti-mouse CD11b (M1/70) | eBioscience | Cat #47–0112-82; RRID:AB_1603093 |
| FITC Anti-mouse CD11b (M1/70) | eBioscience | Cat #12–0112-83; RRID:AB_2734870 |
| PE Anti-mouse CD11b (M1/70) | eBioscience | Cat #11–0112-85; RRID:AB_464936 |
| PE/Cy7 Anti-mouse CD16/32 (FcγRII/III; 93) | BioLegend | Cat #101318; RRID:AB_2104156 |
| PerCP/Cy5.5 Anti-mouse CD16/32 (FcγRII/III; 93) | BioLegend | Cat #101324; RRID:AB_1877267 |
| Biotin Anti-mouse CD34 (RAM34) | eBioscience | Cat #13–0341-85; RRID:AB_466426 |
| Alexa Fluor 700 Anti-mouse CD34 (RAM34) | eBioscience | Cat #56–0341-82; RRID:AB_493998 |
| FITC Anti-mouse CD34 (RAM34) | eBioscience | Cat #11–0341-85; RRID:AB_465022 |
| APC Anti-mouse CD41 (MWReg30) | Biolegend | Cat #133913; RRID:AB_1112675 1 |
| FITC Anti-mouse CD43 (R2/60) | eBioscience | Cat #11–0431-85; RRID:AB_465041 |
| PE Anti-mouse CD43 (R2/60) | eBioscience | Cat #12–0431-83; RRID:AB_465660 |
| APC eFluor 780 Anti-mouse CD45.1 (A20) | eBioscience | Cat #47–0453-82; RRID:AB_1582228 |
| Alexa Fluor 700 Anti-mouse CD45.2 (104) | BioLegend | Cat #109822; RRID:AB_493731 |
| FITC Anti-mouse CD45.2 (104) | BioLegend | Cat #109806; RRID:AB_313443 |
| APC Anti-mouse CD45R (B220) (RA3–6B2) | eBioscience | Cat #17–0452-83; RRID:AB_469396 |
| FITC Anti-mouse CD45R (B220) (RA3–6B2) | eBioscience | Cat #11–0452-85; RRID:AB_465055 |
| PE Anti-mouse CD45R (B220) (RA3–6B2) | eBioscience | Cat #12–0452-85; RRID:AB_465673 |
| PerCP-Cyanine5 Anti-mouse CD45R (B220) (RA3–6B2) | eBioscience | Cat #45–0452-82; RRID:AB_1107006 |
| APC Anti-mouse CD48 (HM48–1) | BioLegend | Cat #103412; RRID:AB_571997 |
| FITC Anti-mouse CD48 (HM48–1) | BioLegend | Cat #103404; RRID:AB_313019 |
| PE Anti-mouse CD48 (HM48–1) | BioLegend | Cat #103406; RRID:AB_313021 |
| PE/Cy7 Anti-mouse CD48 (HM48 | BioLegend | Cat #103424; RRID:AB_2075049 |
| FITC Anti-mouse CD71 (R17217) | eBioscience | Cat #11–0711-85; RRID:AB_465125 |
| APC Anti-mouse CD117 (cKit) (2B8) | eBioscience | Cat #17–1171-83; RRID:AB_469431 |
| APC eFluor 780 Anti-mouse CD117 (cKit) (2B8) | eBioscience | Cat #47–1171-82; RRID:AB_1272177 |
| PE-Cyanine7 Anti-mouse CD117 (cKit) (2B8) | eBioscience | Cat #25–1171-82; RRID:AB_469644 |
| PE Anti-mouse CD127 (IL7Rα; A7R34) | BioLegend | Cat #135010; RRID:AB_1937251 |
| APC Anti-mouse CD150 (TC15–12F12.2) | BioLegend | Cat #115910; RRID:AB_493460 |
| PE Anti-mouse CD150 (TC15–12F12.2) | BioLegend | Cat #115904; RRID:AB_313683 |
| PE-Cyanine7 Anti-mouse CD150 (TC15–12F12.2) | BioLegend | Cat #115914; RRID:AB_439797 |
| Brilliant Violet 650 Anti-mouse CD150 (TC15–12F12.2) | BioLegend | Cat #115931 RRID: AB_2562402 |
| APC Anti-mouse Ter119 (TER-119) | Biolegend | Cat #116212; RRID:AB_313713 |
| FITC Anti-mouse Ter119 (TER-119) | Biolegend | Cat #116206; RRID:AB_313709 |
| PE Ter119 (TER-119) | Biolegend | Cat #116208; RRID:AB_313709 |
| APC Anti-mouse Sca-1 (D7, E13–161.7)\ | eBioscience | Cat #17–5981-82; RRID:AB_469487 |
| Alexa Fluor 700 Anti-mouse Sca-1 (D7, E13–161.7) | eBioscience | Cat #56–5981-82; RRID:AB_657836 |
| FITC Anti-mouse Sca-1 (D7, E13–161.7) | eBioscience | Cat #11–5981-85; RRID:AB_465334 |
| PerCp-Cyanine5.5 Anti-mouse Sca-1 (D7, E13–161.7) | eBioscience | Cat #45–5981-82; RRID:AB_914372 |
| APC Anti-mouse Gr-1 (RB6–8C5) | BioLegend | Cat #108412; RRID:AB_313377 |
| FITC Anti-mouse Gr-1 (RB6–8C5) | BioLegend | Cat #108406; RRID:AB_313371 |
| PE Anti-mouse Gr-1 (RB6–8C5) | BioLegend | Cat #108408; RRID:AB_313373 |
| PE/Cy7 Anti-mouse Gr-1 (RB6–8C5) | BioLegend | Cat #108416; RRID:AB_312663 |
| APC Anti-mouse IgM (II/41) | eBioscience | Cat #17–5790-82; RRID:AB_469458 |
| PE Anti-mouse IgM (II/41) | eBioscience | Cat #12–5790-83; RRID:AB_465941 |
| Recombinant Alexa Fluor 647 Anti-SQSTM1/p62 antibody (EPR4844) | Abcam | Cat # ab194721 |
| Anti-vimentin antibody | Millipore Sigma | Cat #AB5733 |
| Goat anti-chicken IgY (H&L) Alexa Fluor 488 | Invitrogen | Cat #A-11039 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| PIPC | GE Healthcare Biosciences Corp | Cat #27473201 |
| Anti-mouse CD117 microbeads | Miltenyi | Cat #130–091-224 |
| 2-mercaptoethanol | Sigma | Cat #M3148 |
| Heat-inactivated bovine serum | Gibco | Cat #26170043 |
| DMSO | Sigma | Cat #D2650 |
| Baytril | Covetrus | Cat #37713 |
| Ammonium chloride potassium buffer | Covetrus | Cat #37713 |
| Paraformaldehyde | Affymetrix | Cat #19943 |
| 4% paraformaldehyde aqueous solution | Electron Microscopy Sciences | Cat #157–4 |
| PBS | Corning | Cat #MT21040CV |
| Tween 20 | Sigma | Cat #P9416 |
| 4’,6-diamidino-2-phenylindole (DAPI ) | Life Technologies | Cat #62247 |
| Saponin | Sigma | Cat #47036 |
| Fetal Bovine Serum | Life Technologies | Cat #16000044 |
| Bortezomib | Cell Signaling | Cat #2204S |
| Critical Commercial Assays | ||
| Proteasome-Glo chymotrypsin-like cell based assay | Promega | Cat #G8660 |
| RNeasy Plus Micro Kit | Qiagen | Cat #74034 |
| PROTEOSTAT Aggresome detection kit | Enzo | Cat #ENZ-51035-K100 |
| ProLong Diamond Antifade Mountant | Thermo | Cat #P36965 |
| Deposited Data | ||
| RNA-sequencing data | This manuscript | GEO GSE179415 |
| RNA-sequencing data for human HSCs and progenitors | Xie et al, 2019 | GEO: GSE125345 |
| RNA-sequencing data for human HSCs and progenitors | Laurenti et al, 2013 | GEO: GSE42414 |
| RNA-sequencing data for mouse HSCs and progenitors | Signer et al, 2016 | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: B6: C57BL/6J | The Jackson Laboratory |
Cat #000664; RRID:IMSR_JAX:0 00664 |
| Mouse: B6SJL: B6.SJL | The Jackson Laboratory | Cat #002014; RRID:IMSR_JAX:0 02014 |
| Mouse: C57BL/6-Tg(CAG- RFP/EGFP/Map1lc3b)1Hill/J |
The Jackson Laboratory | Cat #027139; RRID:IMSR_JAX:0 27139 |
| Mouse: Bag3fl/fl | Fang et al, 2017 | N/A |
| Mouse: Atg5fl/fl | Hara et al, 2006 | N/A |
| Mouse: Mx1-Cre: B6.Cg-Tg(Mx1-cre)1Cgn/J | The Jackson Laboratory | Cat #003556 RRID:IMSR_JAX:0 03556 |
| Software and Algorithms | ||
| FlowJo | FlowJo, LLC | https://www.flowjo.com/solutions/flowjo/downloads |
| FACSDiva | BD Bioscience | https://www.bdbiosciences.com/enus/products/software/instrumentsoftware/bdfacsdiva-software |
| Prism 8 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Image Lab 6.0.1 | Bio-Rad | https://www.biorad.com/enus/product/image-lab-software?ID=KRE6P5E8Z |
| TopHat 1.4.1 | JHU CCB | https://ccb.jhu.edu/software/tophat/downloads/ |
| STAR 2.6.1 | N/A | https://github.com/alexdobin/STAR |
| PRINSEQ Lite 0.20.3 | N/A | https://sourceforge.net/projects/prinseq/files/standalone/ |
| Htseq-count 0.7.1 | N/A | https://htseq.readthedocs.io/en/master/install.html |
| featureCounts 1.6.5 | N/A | https://sourceforge.net/projects/subre ad/files/subread1.6.5/ |
| Bioconductor package DESeq2 1.24.0 | Bioconductor | https://git.bioconductor.org/packages/DESeq2 |
| Matplotlib | J.D Hunter, 2007 | https://matplotlib.org/stable/index.html |
| ELDASoftware | Hu and Smyth, 2009 | https://bioinf.wehi.edu.au/software/elda/ |
| ZEN (black edition) | Zeiss | https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html |
| ZEN (blue edition) | Zeiss | https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html |