KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-mouse Ter119 Biotin (clone TER-119) | eBioscience | Cat#13-5921-85; RRID:AB_466798 |
| Anti-mouse NK1.1 Biotin (clone PK136) | eBioscience | Cat#13-5941-85; RRID:AB_466805 |
| Anti-mouse Gr-1 Biotin (clone RB6–8C5) | eBioscience | Cat#13-5931-86; RRID:AB_466802 |
| Anti-mouse CD11c Biotin (clone N418) | eBioscience | Cat#13-0114-85; RRID:AB_466364 |
| Anti-mouse CD11b Biotin (clone M1/70) | eBioscience | Cat#13-0112-86; RRID:AB_466361 |
| Anti-mouse CD19 Biotin (clone 1D3/6D5) | eBioscience | Cat#13-0193-85; RRID:AB_657658 |
| Anti-mouse CD3e Biotin (clone 145-2 C11) | eBioscience | Cat#13-0031-85; RRID:AB_466320 |
| Anti-human/mouse B220 Biotin (clone RA3-6B2) | eBioscience | Cat#13-0452-85; RRID:AB_466450 |
| Anti-human/mouse CD44 eFluor 450 (clone IM7) | eBioscience | Cat#48-0441-82; RRID:AB_1272246 |
| Anti-mouse CD25 APC-eFluor 780 (clone PC61.5) | eBioscience | Cat#47-0251-82; RRID:AB_1272179 |
| Streptavidin PerCP-Cyanine5.5 | Biolegend | Cat#405214; RRID:AB_2716577 |
| APC Annexin V | Biolegend | Cat#640919 |
| Bacterial and virus strains | ||
| Stable Competent E.coli | NEB | Cat#C3040 |
| Chemicals, peptides, and recombinant proteins | ||
| Recombinant Human Flt3-Ligand | PreproTech | Cat#300–19 |
| Recombinant Human IL-7 | PreproTech | Cat#200–07 |
| Recombinant Human Stem Cell Factor (SCF) | PreproTech | Cat#300–07 |
| Anti-H3K27me3 antibody | Active Motif | Cat#39156 |
| Retronectin | Takara | Cat#T100B |
| DL1-ext IgG Protein | Gift from Irwin Bernstein (Varnum-Finney et al., 2000) | N/A |
| FuGENE 6 Transfection Reagent | Promega | Cat#E2691 |
| UNC1999 | Caymen Chemical | Cat#14621 |
| GSKJ4 | Caymen Chemical | Cat#12073 |
| IOX1 | Caymen Chemical | Cat#11572 |
| GSK126 | Caymen Chemical | Cat#15415 |
| GSK343 | Caymen Chemical | Cat#14094 |
| Concavalin A | Bangs Laboraatories | Cat#BP531 |
| protein A-MNase | gift from Steven Henikoff (Skene et al., 2018) | N/A |
| Deposited data | ||
| T cell progenitor H3K27me3 CUT&RUN | This paper | Gene Expression Omnibus GSE134749 |
| Thymocyte H3K27ac ChIP-sequencing | Davis et al., 2018 | ENCODE accession ENCSR000CCH |
| Erythroblast H3K9me3 ChIP-sequencing | Davis et al., 2018 | ENCODE accession ENCSR000DHN |
| T cell progenitor H3K27me3 ChIP-sequencing | Zhang et al., 2012 | Gene Expression Omnibus GSE31235 |
| DN3-DP thymocyte Hi-C | Hu etal., 2018 | Gene Expression Omnibus GSE79875 |
| Experimental models: cell lines | ||
| OP9-DL1-GFP | Holmes and Zúñiga-Pflücker, 2009 | N/A |
| Kasumi-1 | ATCC | Cat#CRL-2724; RRID:CVCL_0589 |
| Pheonix-Eco | ATCC | Cat#CRL-3214, RRID:CVCL_H717 |
| Experimental models: organisms/strains | ||
| Mouse: Bcl11bRFP/YFP | Ng et al., 2018 | N/A |
| Oligonucleotides | ||
|
Bcl11b forward primer: TCCACCTACCAGACCCCGAA |
IDT | N/A |
|
Bcl11b reverse primer: CTTCTTCAAAGTGCTTGGCCTC |
IDT | N/A |
|
PAX5 forward primer: CCAGGATGTGCTGCTGTCCCAG |
IDT | N/A |
|
PAX5 reverse primer: CTCCCTGGTGCTGTGCACTGA |
IDT | N/A |
| mir-30-shEed template: TGCTGTTGACAGTGAGCGAAGGCATTATAAGAATAATTAATAGTGAAGCCACAGATGTATTAATTATTCTTATAATGCCTCTGCCTACTGCCTCGGA |
IDT | N/A |
| Recombinant DNA | ||
| pBAD-mTagBFP2 | Addgene | Cat #34632 |
| pMSCV-miR-30 | Gift from Johannes Zuber (Fellmann et al., 2013) | N/A |
| pMSCV-c-Myc-H2B-mCerulean | Kueh et al., 2016 | N/A |
| pBanshee-CFP | Kueh et al., 2016 | N/A |
| pCL-Eco | Imgenex | Cat#NBP2-29540 |
| Software and algorithms | ||
| Software: FlowJo (v10.0.8) | Tree Star | https://www.flowjo.com/ |
| Software: MATLAB (R2018b) | MathWorks | https://www.mathworks.com/products/matlab.html |
| Software: R (v3.9) | N/A | https://www.r-project.org/ |
| Rstudio (v1.2.5042) | N/A | https://rstudio.com/ |
| Ggplot2 (v.3.3) | N/A | https://ggplot2.tidyverse.org/ |
| Bedtools (v2.17.0) | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/ |
| Samtools (v0.1.19-96b5f2294a) | Li et al., 2009 | http://samtools.sourceforge.net/ |
| Fiji (v2.0.0) | Schindelin et al., 2012 | https://imagej.net/Downloads |
| BUnwarpJ | Arganda-Carreras et al., 2006 | https://imagej.net/BUnwarpJ |
| Python(v3.6) | N/A | https://www.python.org |
| Other | ||
| BD FACS Aria III Cell Sorter | BD Biosciences | N/A |
| NucleoSpin PCR Clean-up | Macherey-Nagel | Cat#740609.50 |
| Illumina MiSeq | Illumina | N/A |
| Attune NxT Acoustic Focusing Cytometer | ThermoFisher Scientific | N/A |
| KAPA HyperPrep Kit | Roche | Cat#07962312001 |
| PowerUp SYBR Green Master Mix | ThermoFisher Scientific | Cat#A25741 |
| Ampure XP magnetic beads | Beckman Coulter | Cat#A63880 |
| CFX96 Real-Time PCR Detection System | Bio-Rad | Cat#1855196 |
| CD117 Microbeads | Miltenyi Biotec | Cat#130-091-224 |
| LS Columns | Miltenyi Biotec | Cat#130-042-401 |
| 250mm-diameter PDMS circular micromesh arrays | Microsurfaces Pty Ltd | Cat#MMA-0250-100-08-01 |
| Custom scripts for imaging analysis and simulations | This paper | https://github.com/KuehLabUW/Pease_et_al.2021 |