KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD4 FITC (clone: RPA-T4) | BD Biosciences | Cat#555346; RRID: AB_395751 |
| CD8 PerCP (clone: SK1) | BD Biosciences | Cat#347314; RRID: AB_400280 |
| CD3 APC (clone: UCHT1) | BD Biosciences | Cat#561810; RRID: AB_10893350 |
| CD45 APC/Cy7 (clone: HI30) | Biolegend | Cat#304014; RRID: AB_314402 |
| Glycophorin A PE (clone: 11E4B-7-6 (KC16)) | Beckman Coulter | Cat#IM2211U; RRID: AB_131213 |
| CD34 PerCP-Cy5.5 (clone: 8G12) | BD Biosciences | Cat#347203; AB_400266 |
| CD4 APC (clone: RPA-T4) | BD Biosciences | Cat#555349; RRID: AB_398593 |
| CD 8 APC (clone: SK1) | Biolegend | Cat#344722; RRID: AB_2075388 |
| CD235a APC (clone: GA-R2) | BD Biosciences | Cat#551336; RRID: AB_398499 |
| CD7 FITC (clone: 4H9) | BD Biosciences | Cat#347483; RRID: AB_400309 |
| CD1a PE (clone: HI149) | BD Biosciences | Cat#555807; RRID: AB_396141 |
| CD1a APC (clone: HI149) | Biolegend | Cat#300110; RRID: AB_350438 |
| CD2 FITC (clone: RPA-2.10) | Biolegend | Cat#300206; RRID: AB_314030 |
| CD4 PerCP (clone: RPA-T4) | Biolegend | Cat#300528; RRID: AB_893321 |
| CD7 PE (clone: CD7-6B7) | Biolegend | Cat#343106; RRID: AB_1732011 |
| CD8 PerCP (clone: SK1) | Biolegend | Cat#344708; RRID: AB_1967149 |
| CD34 PE-Cy7 (clone: 581) | Biolegend | Cat#343516; RRID: AB_1877251 |
| CD44 Alexa Fluor 700 (clone: BJ18) | Biolegend | Cat#338813; RRID: AB_2715998 |
| CCR7 APC-Cy7 (clone: G043H7) | Biolegend | Cat#353212; RRID: AB_10916390 |
| CD19 PerCP (clone: SJ25-C1) | BD Biosciences | Cat#340421; RRID: AB_400028 |
| CD7 FITC (clone: CD7-6B7) | Biolegend | Cat#343104; RRID: AB_1659216 |
| CD123 PE (clone: 6H6) | Biolegend | Cat#306005; RRID: AB_314579 |
| CD14 BV605 (clone: 63D3) | Biolegend | Cat#367125; RRID: AB_2716230 |
| CD303 APC (clone: 201A) | Biolegend | Cat#354206; RRID: AB_11150412 |
| HLA-DR FITC (clone: L243) | BD Biosciences | Cat#347363; RRID: AB_400291 |
| CD14 APC (clone: MΦP9) | BD Biosciences | Cat#340436; RRID: AB_400509 |
| CD66b PE-Cy7(clone: G10F5) | Biolegend | Cat#305116; RRID: AB_2566605 |
| CD303 AF 700 (clone: 201A) | Biolegend | Cat#354228; RRID: AB_2629744 |
| CD3 APC (clone: UCHT1) | Biolegend | Cat#300439; RRID: AB_2562045 |
| CD45 PerCP (clone: HI30) | Biolegend | Cat#304026; RRID: AB_893337 |
| CD4 PE (clone: A161A1) | Biolegend | Cat#357409; RRID: AB_2565661 |
| CD8 APC-Cy7 (clone: SK1) | Biolegend | Cat#344714; RRID: AB_2044006 |
| TCRa/b PE (clone: IP26) | Biolegend | Cat#306708; RRID: AB_314646 |
| CD56 PE (clone: HCD56) | Biolegend | Cat#318306; RRID: AB_604101 |
| CD11c APC (clone: 3.9) | Biolegend | Cat#301614; RRID: AB_493023 |
| CD33 PE (clone: P67.6) | BD Biosciences | Cat#347787; RRID: AB_400350 |
| CD56 APC (clone: HCD56) | Biolegend | Cat#318310; RRID: AB_604106 |
| CD45 PerCP (clone: HI30) | Biolegend | Cat#304026; RRID: AB_893337 |
| CD14 FITC (clone: M5E2) | Biolegend | Cat#301804; RRID: AB_314186 |
| CD15 FITC (clone: HI98) | Biolegend | Cat#301904; RRID: AB_314196 |
| CD66b PE (clone: G10F5) | Biolegend | Cat#305106; RRID: AB_305106 |
| CD1a PE (clone: HI149) | Biolegend | Cat#300106; RRID: AB_314020 |
| CD4 PerCP (clone: RPA-T4) | Biolegend | Cat#300528; RRID: AB_893321 |
| CD8 PerCP (clone: SK1) | Biolegend | Cat#344708; RRID: AB_1967149 |
| CD19 PerCP (clone: SJ25-C1) | BD Biosciences | Cat#340421; RRID: AB_400028 |
| CD34 PE-Cy7 (clone: 581) | Biolegend | Cat#343516; RRID: AB_1877251 |
| APC Mouse Anti-Human IRF8 (clone: V3GYWCH) | eBioscience | Cat#17-9852-82; RRID: AB_2573318 |
| Mouse IgG1 K Isotype Control APC (clone: P3.6.2.8.1) | eBioscience | Cat#17-4714-81; RRID: AB_1603315 |
| Biological Samples | ||
| Human Thymuses | Children’s Hospital at Los Angeles | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| HI-FBS | Gemini Bio-products | Cat#100-106 |
| B-27 Supplement | GIBCO | Cat#17504-044 |
| Ascorbic Acid | Gemini Bio-Products | Cat#400-109 |
| FBS Defined | Hyclone | Cat#SH30070.03 |
| IL-7 (used for R-B27 Medium) | Peprotech | Cat#200-07 |
| IL-7 (used for B/NK/M Medium; PDC Differentiation) | Miltenyi Biotec | Cat#130-095-367 |
| Flt-3 ligand (used for R-B27 Medium) | Peprotech | Cat#300-19 |
| Flt-3 (used for B/NK/M Medium; PDC Differentiation) | Miltenyi Biotec | Cat#130-096-474 |
| TPO (used for B/NK/M Medium; PDC Differentiation) | Miltenyi Biotec | Cat#130-094-011 |
| IL-15 (used for NK Medium) | Peprotech | Cat#200-15 |
| SCF (used for NK Medium) | Miltenyi Biotec | Cat#130-096-692 |
| GM-CSF (used for PDC Differentiation) | Peprotech | Cat#300-03 |
| Fixation Buffer | Biolegend | Cat#420801 |
| Cell Staining Buffer | Biolegend | Cat#420201 |
| 10x Permeabilization Wash Buffer | Biolegend | Cat#421002 |
| DAPI | Invitrogen | Cat#D1306 |
| Immune Globulin Intravenous (Human) | Carimune | Cat#44206-417-06 |
| Critical Commercial Assays | ||
| CD34 Microbead Kit | Miltenyi Biotec | Cat#130-100-453 |
| ATO assay: Cell Culture Insert | Millipore | Cat#PICM0RG50 |
| BD genomics Precise WTA Single Cell Kit | BD Biosciences | Cat#634100 |
| Picopure RNA extraction kit | ThermoFisher Scientific | Cat#KIT0204 |
| Smart-Seq V4 ultralow input RNA-Seq kit | Clontech | Cat#634888 |
| Deposited Data | ||
| Human gene annotation GRCh38.p12 (Release 31) | EMBL-EBI | https://www.gencodegenes.org/human/release_31.html |
| Raw and analyzed data | This paper | GEO: GSE139042 |
| GRCh38 version of the human genome (GCA_000001405.15_GRCh38_no_alt_analysis_set.fna) | NCBI | http://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/analysisSet/ |
| Mouse.MitoCarta2.0 database | Broad Institute | https://www.broadinstitute.org/scientific-community/science/programs/metabolic-disease-program/publications/mitocarta/mitocarta-in-0) |
| Jackson database (for conversion of Mouse gene IDs to human gene IDs) | The Jackson Laboratory | http://www.informatics.jax.org/homology.shtml |
| Ensembl (for conversion of Mouse gene IDs to human gene IDs) | EMBL-EBI | http://www.ensembl.org/biomart/martview/f21f6d3f6c139e32bd08fb6fbe59b5e8 |
| Experimental Models: Cell Lines | ||
| Human MS5 cell line | Gay M. Crooks Laboratory | Seet et al. 2017 |
| Human MS5-DLL cell line | Gay M. Crooks Laboratory | Seet et al. 2017 |
| Software and Algorithms | ||
| Cellranger (v2.2.0 and v3.0.2) | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation |
| BDTM Precise WTA Analysis (v2.0) | SevenBridges | https://www.sevenbridges.com/ |
| inDrop (v2 and v3) | GitHub | https://github.com/indrops/indrops |
| Seurat (v2.3.4) | Bultler et al., 2018 | http://satijalab.org/seurat/ |
| Scrublet | Wolock et al., 2019b | https://github.com/AllonKleinLab/scrublet |
| BNOmics | Gogoshin et al., 2017 | https://omictools.com/bnomics-tool |
| Monocle (v3) | Cao et al., 2019 | https://cole-trapnell-lab.github.io/monocle3/docs/trajectories/ |
| tradeSeq | Van den Berge et al., 2020 | https://github.com/statOmics/tradeSeq |
| GSEA v4.0 | Subramanian et al., 2005 | https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/GSEA_v4.0.x_Release_Notes |
| DAVID | Huang da et al., 2009 | https://david.ncifcrf.gov/ |
| Galaxy | N/A | https://usegalaxy.org/ |
| Trimmomatic (Galaxy version 0.38.0) | Bolger et al., 2014 | https://toolshed.g2.bx.psu.edu/repository?repository_id=ef9e620e9ac844b3 |
| TopHat (Galaxy version 2.1.1) | Kim et al., 2013 | https://toolshed.g2.bx.psu.edu/repository?repository_id=3bece861a6a3608c |
| Samtools (Galaxy version 2.0.3) | Li et al., 2009 | https://toolshed.g2.bx.psu.edu/repository?repository_id=67974b61f56a2c93 |
| HTseq (Galaxy version 0.9.1) | Anders et al., 2015 | https://toolshed.g2.bx.psu.edu/repository?repository_id=2df7e24ce6c1f224 |