KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD16/32 Fc Block | Biolegend | Cat# 562440 |
| CD19 | BD biosciences | Cat# 562440 |
| CD93 | Biolegend | Cat# 136506 |
| IgM Fab fragment | Jackson ImmunoResearch | Cat# 115–607-020 |
| CD2 | Biolegend | Cat# 100108 |
| CD43 | BD biosciences | Cat# 563206 |
| H3K4me1 | abcam | Ab8895 |
| anti-CD19 conjugated MACS beads | Miltenyi Biotech | 130–052-201 |
| Bacterial and Virus Strains | ||
| Rag1-expressing retrovirus | This paper | |
| Cre-expressing retrovirus | This paper | |
| Biological Samples | ||
| B6 CD19+ cells (bone marrow) | This paper | |
| E88Δ CD19+ cells (bone marrow) | This paper | |
| small E88Δ CD19+ cells (bone marrow) | This paper | |
| g3-g4Δ CD19+ cells (bone marrow) | This paper | |
| g3-USΔ CD19+ cells (bone marrow) | This paper | |
| g3-DSΔ CD19+ cells (bone marrow) | This paper | |
| B6.Rag1−/− CD19+ cells (bone marrow) | This paper | |
| E88Δ.Rag1−/− CD19+ cells (bone marrow) | This paper | |
| B6.Rag−/− Igh-Tg+ CD19+ cells (bone marrow) | This paper | |
| E88Δ.Rag−/−Igh-Tg+ CD19+ cells (bone marrow) | This paper | |
| B6 CD19+ cells (spleen) | This paper | |
| E88Δ CD19+ cells (spleen) | This paper | |
| B6 CD19+ cells (liver E17) | This paper | |
| E88Δ CD19+ cells (liver E17) | This paper | |
| B6 pro-B cells (bone marrow) see sorting scheme Figure S4A | This paper | |
| E88Δ pro-B cells (bone marrow) see sorting scheme Figure S4A | This paper | |
| B6 small pre-B cells (bone marrow) see sorting scheme Figure S4A | This paper | |
| E88Δ small pre-B cells (bone marrow) see sorting scheme Figure S4 | This paper | |
| Chemicals, Peptides, and Recombinant Proteins | ||
| STI571 (Gleevec) | Toronto Research Chemicals | Cat#407000 |
| Formaldehyde 37% | Fisher Scientific | BP531–25 |
| RPMI Medium 1640 | Gibco | 11875–093 |
| BglII (Restriction Endonuclease) | NEB | R0144S |
| Blasticidin | Lifetech Invitrogen | R21001 |
| NlaIII (Restriction Endonuclease) | NEB | R0125S |
| Critical Commercial Assays | ||
| DNeasy Blood & Tissue Kit | QIAGEN | Cat#69504 |
| RNeasy Plus Mini Kit | QIAGEN | Cat#74134 |
| QIAshredder | QIAGEN | Cat#79654 |
| QuantiTect® Reverse Transcription | QIAGEN | Cat#205313 |
| TaqMan™ Fast Universal PCR Master Mix (2X) | Applied Biosystems | Cat# 4352042 |
| SYBR Green Master Mix | Bio-rad | Cat#1725270 |
| Expand™ Long Template PCR System | Roche | Cat#11681842001 |
| SYBR Green Master Mix | Biotool | Cat#B21203 |
| Deposited Data | ||
| See Table S2 | ||
| Experimental Models: Cell Lines | ||
| Abelson virus transformed pro-B cell lines 445.3 (Rag1−/−) | (Kumar et al., 2013) | |
| Abelson virus transformed pro-B cell lines 22D6 | (Yancopoulos and Alt, 1985) | |
| 445.3-E88Δ.Rag−/− | This paper | |
| J558 | ATCC ® | TIB-6 |
| EL4 | ATCC ® | TIB-39 |
| 293T | ATCC® | CRL-3216™ |
| Experimental Models: Organisms/Strains | ||
| C57BL/6 | Jackson Labs | |
| C57BL/6 E88Δ | This paper | |
| C57BL/6 small E88Δ | This paper | |
| C57BL/6 g3-g4Δ | This paper | |
| C57BL/6 g3-USΔ | This paper | |
| C57BL/6 g3-DSΔ | This paper | |
| B6.Rag1−/− | Jackson Labs | |
| E88Δ.Rag1−/− | This paper | |
| B6.Rag−/−Igh-Tg+ | (Nussenzweig et al., 1987) | |
| E88Δ.Rag−/−Igh-Tg+ | This paper | |
| Oligonucleotides | ||
| See Table S1 for sequences and details | ||
| Recombinant DNA | ||
| pCAG-EGxxFP | (Mashiko et al., 2013) | |
| pX330-U6-Chimeric_BB-CBh-hSpCas | (Cong et al., 2013) | Addgene Plasmid #42230 |
| pX335-U6-Chimeric_BB-CBh-hSpCas9n | (Cong et al., 2013) | Addgene Plasmid #42335 |
| pMSCV-IRES-Bsr- Rag1 | Dr. David Schatz (Yale Universisy) | |
| MSCV-IRES-GFP | Plasmid #20672 | Addgene Plasmid #20672 |
| pEco | CloneTech | 631530 |
| MCS1-EF1α-RFP-T2A-Puro-pA-MCS2 | System Biosciences | HR110PA-1 |
| pGL3 vector | Promega | E1751 |
| Software and Algorithms | ||
| Cutadapt v1.14 | (Martin, 2011) | |
| Bowtie2 v2.2.9 | (Langmead and Salzberg, 2012) | |
| Bedtools v2.17.0 | (Quinlan and Hall, 2010) | |
| UCSC Genome Browser software | The University of California, Santa Cruz | |
| DESeq2 | (Love et al., 2014) | |
| Other | ||