Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| c-kit (CD117) APC | eBioscience | Cat# 17-1171; clone 2B8; RRID:AB_469429 |
| Sca1 APC-Cy7/FITC | BD Bioscience | Cat# 560654; clone D7; RRID:AB_1727552/ Cat# 11-5981-82; clone D7; RRID:AB_465333 |
| CD150 Pe-Cy5 | Biolegend | Cat# 115912; clone TC15-12F12.2; RRID:AB_493598 |
| CD48 PacBlue/PE | Biolegend | Cat# 103427; clone HM48-1; AB_10895922/ Cat# 12-0481; clone HM48-1; RRID:AB_465694 |
| CD34 FITC | eBioscience | Cat# 2159106; clone RAM34 |
| CD41 PE/PacBlue | Biolegend | Cat# 12-0411-82 clone eBioMWReg30(MWRe g30); RRID:AB_763485/ Cat# 48-0411-80; clone eBioMWReg3; RRID:AB_1582239 |
| Ki67 FITC | eBioscience | Cat# 556026; clone B56; RRID:AB_396302 |
| CD5 Pe-Cy7 | eBioscience | Cat# 25-0051-81 clone 53-73 RRID:AB_657755 |
| CD8a Pe-Cy7/PE | eBioscience | Cat# 25-0081; clone 53-6.7; RRID:AB_469584/ Cat# 12-0081; clone 53-6.7; RRID:AB_465530 |
| CD11b Pe-Cy7/APC/APC-Cy7 | eBioscience | Cat# 25-0112; clone M1/70; RRID:AB_469588/ Cat# 17-0112; clone M1/70; /Cat# 47-0112; clone M1/70; RRID:AB_1603193 |
| B220 Pe-Cy7/PE/APC-Cy7 | eBioscience | Cat# 25-0452-82; clone Ra3-6B2; RRID:AB_469627/ Cat# 12-0452; clone Ra3-6B2; RRID:AB_465671/ Cat# 47-0452; clone Ra3-6B2; RRID:AB_1518810 |
| Gr1 Pe-Cy7/APC-Cy7 | eBioscience | Cat# 25-5931; clone RB6-8C5; RRID:AB_469663/ Cat# 47-5931; clone RB6-8C5; RRID:AB_1518804 |
| Ter119 Pe-Cy7/FITC | eBioscience | Cat#25-5921; clone TER119; RRID:AB_469661/ Cat# 11-5921; clone TER119; RRID:AB_465311 |
| Streptavidin Pe-Cy7/PE | eBioscience | Cat# 405206; clone S3E11/Cat# 12-4317-87; clone S3E11 |
| CD16/32 eFluor450 | eBioscience | Cat# 57-0161; clone 93 |
| CD127 PE | eBioscience | Cat# 12-1273-83; clone eBioSB/199 (SB/1999); RRID:AB_953564 |
| CD4 PE | eBioscience | Cat# 12-0041; clone GK1.5; RRID:AB_465506 |
| CD71 PE | eBioscience | Cat# 12-0711-83; clone R17217(R17 217.1.4); RRID:AB_465741 |
| CD42d APC | eBioscience | Cat# 17-0421-82; clone 1C2; RRID:AB_1724071 |
| CD45.1 PacBlue | eBioscience (BD) | Cat# 110722; clone A20; RRID:AB_492866/ |
| CD45.2 FITC/AF700 | eBioscience | Cat# 11-0454; clone 104; RRID:AB_465061/ Cat# 560693; clone 104; RRID:AB_1727491 |
| Alexa Fluor 647-anti-CD144 FITC | Biolegend | Cat# 138005; clone BV13; RRID:AB_10568319 |
| Alexa Fluor 647-anti-CD31 BV 421 | Biolegend (BD) | Cat# 562939; clone MEC13.3; RRID:AB_2665476 |
| Bacterial and virus strains | ||
| Mycobacterium avium | Matatall et al., 2016 | SmT 2151 |
| Chemicals, peptides, and recombinant proteins | ||
| polyinosinic:polycytidylic acid (pI:pC) | InvivoGen | Tlrl-pic-5 |
| PBS | Sigma Aldrich | D8537-6X500ML |
| clarithromycin | Sigma | 81103-11-9 |
| ACK lysing buffer | Lonza | 10-548E |
| BD Cytofix/Cytoperm | BD Bioscience | 561651 |
| PermWash | (BD Bioscience) | BD 554723 |
| Hoechst33342 | Invitrogen | H3570 |
| Histopaque 1083 | Invitrogen | SD10831 A |
| Hematoxylin/Eosin | Sigma-Aldrich Chemie GmbH/Sigma | 51275-1L/ HT110232 |
| Ethylenediaminetetraacetic acid (EDTA) | Sigma-Aldrich | ED2SS-1KG |
| Iscove’s modified Dulbecco’s medium (IMDM) | Life Technologies | 21980065 |
| 7-AAD, | Invitrogen/ Life Technologies | A1310 |
| StemSpan SFEM) | StemCell | 09650 |
| Flt3-Ligand | PeproTech | 300-19-100 |
| TPO | PeproTech | 315-14 |
| IL-3 | PeproTech | 213-13-50 |
| IL-11 | PeproTech | 220-11-100 |
| Epo | Janssen | 06301240 |
| IL-7 | PeproTech | 217-17-10 |
| SCF | PeproTech | 250-03-100 |
| Critical commercial assays | ||
| Biotin Binder Dynabeads | Life Technologies | 11415D |
| QIAamp DNA Micro Kit | Qiagen | 56304 |
| SMARTer Ultra Low RNA kit | Clontech | 634888 |
| ERCC RNA spike-ins | ThermoFisher Scientific | 4456740 |
| Illumina Nextera XT kit | Illumina | 4456740 |
| Deposited data | ||
| Whole genome bisulfite sequencing data for LT-HSC isolated from aged and pI:pC/CON treated mice | This manuscript | NCBI Gene Expression Omnibus (GEO) GSE200337 |
| Whole genome bisulfite sequencing data for LT-HSC isolated from young mice | This manuscript | NCBI Gene Expression Omnibus (GEO) GSE52709 |
| scRNA-seq data | This manuscript | NCBI Gene Expression Omnibus (GEO)GSE200979 |
| Experimental models: Organisms/strains | ||
| C57BL/6 | Harlan Laboratories, Charles River Laboratories, or Janvier Laboratories | |
| B6.SJL-Ptprca Pepcb/BoyJ | Harlan Laboratories, Charles River Laboratories, or Janvier Laboratories | |
| ROSA26+/ConfettiFlk-1+/Cre (Conf-Flk-1Cre) | Ganuza et al., 2019 | |
| Scl-tTA;H2BGFP | Wilson et al., 2008 | |
| Software and algorithms | ||
| web-based ELDA software | http://bioinf.wehi.edu.au/software/elda/ | |
| FlowJo software | Tree Star | |
| Slide Book software | Intelligent Imaging Innovations | |
| ZEN 2011 (blue edition) 1.0 | Zeiss | |
| Roddy Workflow | https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows | |
| ’BWA-MEM’ | https://arxiv.org/abs/1303.3997 | |
| SAMtools flagstat | Li et al., 2009 | |
| ‘bistro’ methylation caller (version 0.2.0) | https://github.com/stephenkraemer/bistro | |
| Zeiss AxioVision 4.8 software | Zeiss | |
| Fiji (ImageJ) | https://imagej.nih.gov/ij/ | |
| STAR (Spliced Transcript Alignment to a Reference) | Dobin et al., 2013; | version 2.5 |
| Destiny R package | Angerer et al., 2016 | https://bioconductor.org/packages/release/bioc/html/destiny.html |
| GraphPad Prism software | GraphPad Software, Inc., SanDiego, CA | http.//www.graphpad.com |
| R software | https://www.r-project.org/ | |
| Other | ||
| Hemavet 950 FS veterinary blood cell counting machine | Drew Scientific | |
| LSRFortessa cytometer | Becton Dickinson | |
| LSRII | Becton Dickinson | |
| FacsAria I, II or III flow cytometer) | BD Bioscience | |
| ZEISS AXIO examiner D1 microscope | ZEISS | |
| confocal scanner unit, | Yokogawa | CSUX1CU |
| Axio Plan Zeiss Microscope | Zeiss | version 4.1.0 |
| Axio Cam ICc3 | Zeiss | |
| Tissue-TeK-VIP Sakura tissue processor | ||
| HistoStar embedding workstation | Thermo Scientific | |
| Microtome | Thermo Scientific | Microm HM 355S |
| HiSeq 2000 platform | Illumina | |
| CellObserver system | Zeiss | |
| Fluidigm C1 system | Fluidigm | |