KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD3e 145-2C11 | eBioscience | 14-0031-82; RRID:AB_2621636 |
| CD4 GK1.5 | Tonbo, BD Bioscience | 20-0041; RRID:AB_11205236 |
| CD5 53-7.3 | eBioscience | 17-0051-82; RRID: AB_469331 |
| CD8a 53-6.7 | Tonbo | 50-0081; RRID: AB_10596646 |
| CD11b M1/70 | Biolegend, Tonbo, BD Bioscience | 101206; RRID: AB_312789, 35-0112; RRID: AB_2621676, 563553; RRID: AB_2738276 |
| CD19 1D3 | eBioscience, Tonbo | 50-0193; RRID: AB_2621752 |
| CD21 7E9, 4E3 | Biolegend, eBioscicence | 123407; RRID: AB_940403, 11-0212; RRID: AB_464977 |
| CD24 M1/69 | eBioscience | 45-242-82; RRID:AB_1210701 |
| CD25 PC61.5 | Biolegend, eBioscience | 102005; RRID: AB_312854, 12-0251-82; RRID: AB_465607 |
| CD41 MWReg30 | eBioscience | 110411-82; RRID: AB_10639937 |
| CD43 S11 | Biolegend | 143219; RRID: AB_2800666 |
| CD44 IM7 | eBioscience, BD Bioscience | 25-0441-82; RRID: AB_469623, 560569; RRID: AB_1727484 |
| CD93 AA4.1 | eBioscience, Biolegend | 17-5892-82; RRID: AB_469466, 136511; RRID: AB_2275879 |
| CD117 2B8 | eBioscience, Biolegend | 25-1171-82, 105826; RRID: AB_1626278 |
| CD150 TC15-12F12.2 | Biolegend | 115910; RRID: AB_493461 |
| CD45 30-F11 | BD Bioscience, Biolegend, Tonbo | 552848; RRID: AB_394489, 103112; RRID: AB_312977, 35-0451; RRID: AB_469717 |
| CD45.1 A20 | BD Bioscience, eBioscience | 565212; RRID:AB_2722493, 47-0453-82; RRID: AB_1582228 |
| CD45.2 104 | BD Bioscience, Biolegend | 564616; RRID: AB_2738867, 109806; RRID: AB_313443 |
| IgM II/41, RMM-1 | BD Bioscience, Biolegend | 743329; RRID: AB_2741430, 406506; RRID: AB_315056 |
| IgD 11-26c.2a | Biolegend | 405720; RRID: AB_2561876 |
| B220 RA3-6B2 | Tonbo, Biolegend | 60-0452; RRID: AB_2621849, 103207; RRID: AB_312992 |
| FcERI MAR-1 | Biolegend, Tonbo | 134319; RRID: AB_10641135, 35-5898; RRID: AB_2621719 |
| F4/80 BM8 | eBioscience | 47-4801-82; RRID: AB_1548745 |
| CCR6 140706 | BD Bioscience | 561751; RRID: AB_10896986 |
| Gr-1 RB6-8C5 | Biolegend | 108428; RRID: 893558 |
| EPCR 1560 | eBioscience | 12-2012-82; RRID: AB_914317 |
| CD144 11D4.1 | BD Bioscience | 562242; RRID: AB_2737608 |
| CD48 HM48-1 | Biolegend, BD Bioscience | 103404; RRID: AB_313019, 740236; RRID: AB_2739984 |
| CD23 B3B4 | eBioscience | 25-0232-82; RRID: AB_469604 |
| CD127 A7R34 | Biolegend, eBioscience | 135012; RRID: AB_1937216, 12-1271-82; RRID: AB_465844 |
| Ter119 TER-119 | Tonbo, Biolegend, eBioscience | 65-5921; RRID: AB_2935630, 116223; RRID:AB_2137788, 11-5921-82; RRID:AB_465311 |
| Sca-1 D7 | eBioscience, Biolegend | 25-5981-82; RRID: AB_469669, 108124; RRID:AB_893615 |
| CD34 RAM34 | eBioscience | 11-0341-82; RRID: AB_465021 |
| Thy1.2 30-H12 | Biolegend, eBioscience | 105328; RRID: AB_10613293, 11-0902-82; RRID:AB_465154 |
| CD184 2B11 | eBioscience | 12-9991-82; RRID: 891391 |
| Chemicals, peptides, and recombinant proteins | ||
| Tamoxifen | Sigma | T5648 |
| Progesterone | Sigma | P0130 |
| Recombinant mouse IL-7 | PeproTech | 217-17 |
| Recombinant mouse SCF | PeproTech | 250-03 |
| Recombinant mouse Flt3-ligand | PeproTech | 250-31L |
| Collagenase Type I (0.25%) | STEMCELL Technologies | 07902 |
| Critical commercial assays | ||
| SMART-Seq V4 Ultra Low RNA Kit | Takara | # 634898 |
| MethoCult M3630 | STEMCELL Technologies | 03630 |
| Deposited data | ||
| scRNA-sequencing | GEO database | GSE182206 |
| Experimental models: Cell lines | ||
| OP-9 stromal cells | Dr. Toru Nakano at Osaka University, Japan | ATCC CRL-2749 |
| Experimental models: Organisms/strains | ||
| Fgd5ZsGreen-CreERT2 | C57BU6N-Fgd5tm3(cre/ERT2)Djr/J | Jackson no. 027789 |
| Cdh5(PAC)-CreERT2 | C57BL/6-Tg(Cdh5-cre/ERT2) | Taconic no. 13073 |
| Rosa-TdTomato | B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J | Jackson no. 007909 |
| NSG | NOD.Cg-PrkdcscidIl2rgtm1wjl/Szj | Jackson no. 005557 |
| Boy/J | B6.SJL-PtprcaPepcb/BoyJ | Jackson no. 002014 |
| Software and algorithms | ||
| Fastqc | Babraham Institute | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| STAR | PMID: 23104886 | https://github.com/alexdobin/STAR |
| Htseq-count | PMID: 25260700 | https://github.com/htseq/htseq |
| SC3 | PMID: 28346451 | http://bioconductor.org/packages/release/bioc/vignettes/SC3/inst/doc/SC3.html |
| Monocle2 | PMID: 28825705 | http://cole-trapnell-lab.github.io/monocle-release/docs/ |
| CellRanger | PMID: 28091601 | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorials |
| Scikit-learn | https://scikit-learn.org/stable/ | |
| Velocyto.py | PMID: 30089906 | http://velocyto.org/velocyto.py/tutorial/analysis.html |
| velocyto.R | https://github.com/velocyto-team/velocyto.R | |
| scVelo | Volker Bergen | https://scvelo.readthedocs.io |
| Script used for Figures 5A and 5D | This paper | https://github.com/seitalab/hsc_independent |
| Approximate Bayesian Computation (Figure S6) | This paper | https://github.com/djhshih/analysis-lineage-tracing-b1a |