Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-CD180 (RP105) | BD PharMingen | Cat# 552128 |
| SP1 | Abcam | Cat# ab13370 |
| MAZ | Bethyl Laboratories | Cat # A301-652A |
| E2F4 | ENCODE | ENCSR000ERU |
| IRF4 | Santa Cruz Biotech. | Cat# sc-6059 |
| NRF1 | Abcam | Cat# ab34682 |
| JUND | ENCODE | ENCSR000ERR |
| YY1 | Abcam | Cat# ab109237 |
| RREB1 | Bethyl Laboratories | Cat# A303-129A |
| EGR1 | Cell Signaling | Cat# 4153S |
| PU.1 | Santa Cruz Biotech. | Cat# sc-352 X |
| RELA | Santa Cruz Biotech. | Cat# sc-372 |
| Bacterial and virus strains | ||
| One shot Stbl3 E. coli | Thermo Fisher | C737303 |
| 10-beta competent E. coli | NEB | C3019H |
| Chemicals, peptides, and recombinant proteins | ||
| IL-4 from mouse | Sigma | Cat# SRP3211 |
| LPS | Sigma | Cat# L2630 |
| FBS | Gemini | Cat# 100-500 |
| RPMI 1640 | Invitrogen (Gibco) | Cat#R7388 |
| penicillin/streptomycin | Invitrogen (Gibco) | Cat#15070063 |
| 2-beta mercaptoethanol | Invitrogen (Gibco) | Cat# 21985-023 |
| puromycin | Sigma | Cat#P8833 |
| 37% formaldehyde | Sigma | Cat# F1635 |
| Agencourt AMPure XP | Beckman Coulter | A63882 |
| DMEM (Dulbecco~s Modified Eagle Medium) | Thermo Fisher | 11960-044 |
| DMEM, low glucose pyruvate | Thermo Fisher | 11885084 |
| Dynabeads MyOne Streptavidin T1 | Thermo Fisher | 65601 |
| Dynabeads Protein A | Thermo Fisher | 10002D |
| Dynabeads Protein G | Thermo Fisher | 10004D |
| Dynabeads M-280 streptavidin | Thermo Fisher | 11205D |
| EDTA 0.5M | Thermo Fisher | 15575020 |
| Fetal Bovine Serum, BenchMark | Gemini - Bio Products | 100-106 |
| Fetal Bovine Serum, ES Cell qualified | ATCC | SCRR-30-2020 |
| GlutaMAX | Thermo Fisher | 35050061 |
| HEPES | Thermo Fisher | 15630-080 |
| Janelia Fluor 549 HaloTag Ligand | Promega | GA1111 |
| Lipofectamine™ LTX Reagent with PLUS™ Reagent | Thermo Fisher | 15338100 |
| MEM Non-Essential Amino Acids | Thermo Fisher | 11140-050 |
| NucSpot Live 488 Nuclear Stain | Biotium | 40081 |
| Opti-MEM® I Reduced Serum Medium | Thermo Fisher | 31985-070 |
| PA Janelia Fluor 549 HaloTag Ligand | Jiji Chen | N/A |
| Penicillin-Streptomycin | Thermo Fisher | 15140122 |
| Proteinase K | Thermo Fisher | 26160 |
| Puromycin | LifeTechnologies | A11138-03 |
| Q5 High-Fidelity DNA polymerase | New England Biolabs | M0491L |
| Sodium Dodecyl Sulfate Solution, 10X | Thermo Fisher | 27730020 |
| Sodium Pyruvate | Thermo Fisher | 11360-070 |
| Glycine | Sigma | Cat#50046 |
| Mithramycin analogue | Francisco Moris | EC-8042 |
| Critical commercial assays | ||
| EasySep™ Mouse B Cell Isolation Kit | Stemcell technologies | 19854 |
| Genomic extraction kit | Biotool™ | B4001 |
| Ovation Ultralow Library System V2 | Nugen | 344 |
| ChIP DNA clean and concentrator | ZymoResearch | Cat # 11379 |
| RNAeasy kit | Qiagen | Cat# 74104 |
| DNeasy blood and tissue kit | Qiagen | Cat #69504 |
| MinElute PCR purification kit | Qiagen | Cat# 28004 |
| Nucleofector Kit V | Lonza | Cat# VCA-1003 |
| Tagment DNA Enzyme and Buffer (ATAC-seq) | Illumina | Cat3 20034210 |
| CloneAmp HiFi PCR Premix | TaKaRa | 639298 |
| NEBNext Ultra II Directional RNA Library Prep Kit for Illumina | New England Biolabs | E7760 |
| NEBuilder HiFi DNA Assembly Cloning Kit | New England Biolabs | E5520S |
| Qubit ds DNA HS assay kit | Thermo Fisher | Q32851 |
| RNAqueous™-Micro Total RNA Isolation Kit | Thermo Fisher | AM1931 |
| SF Cell Line 4D-Nucleofector™ X Kit | Lonza | V4XC-2032 |
| SuperScript III First-Strand Synthesis System | Life Technologies | 18080-051 |
| ZR Plasmid Miniprep | Zymo Research | D4015 |
| NEBNext poly(A) mRNA Magnetic Isolation Module | New England Biolabs | E7490L |
| Ultralow DNAseq kits | Nugen | 0344NB-A01 |
| Tn5 transposase; Nextera® DNA Library Preparation Kit | Illumina | FC-121-1030 |
| Deposited data | ||
| Raw and analyzed data | This paper | GSE164906 |
| Imaging data | This paper |
https://data.mendelev.com/datasets/4k2xrcmjwg/1
https://data.mendeley.com/datasets/9fmpt74b6y/1 |
| Experimental models: Cell lines | ||
| Mouse: primary splenic B cells | This paper | N/A |
| Mouse: CH12B lymphoma cell line | Tasuku Honjo | N/A |
| Human: PlatA retroviral packaging cell line | Cell Biolabs Inc. | RV-102 |
| Human: PlatE retroviral packaging cell line | Cell Biolabs Inc. | RV-101 |
| CH12 Halotag-Smad3 cell line | This paper | N/A |
| CH12 Halotag-Smad7 cell line | This paper | N/A |
| CH12 Zbtb7a−/− cell line | This paper | N/A |
| CH12 Maz−/− cell line | This paper | N/A |
| CH12 Klf16−/− cell line | This paper | N/A |
| CH12 Sp1−/− cell line | This paper | N/A |
| CH12 Sp1−/− Zbtb7a−/− double KO cell line | This paper | N/A |
| CH12 Klf16−/− Zbtb7a−/− double KO cell line | This paper | N/A |
| CH12 Sp1−/− Klf16−/− Zbtb7a−/− triple KO cell line | This paper | N/A |
| CH12 Sp1−/− Klf16−/− Zbtb7a−/− Maz−/− quadruple KO cells | This paper | N/A |
| Experimental models: Organisms/strains | ||
| C57BL6 | Jackson Laboratory | JAX:000664 |
| CAST/EiJ | Jackson Laboratory | JAX:000928 |
| BALB/cJ | Jackson Laboratory | JAX:000651 |
| CAST/EiJ X BALB/cJ F1 progeny | This paper | N/A |
| C57BL/6J X BALB/cJ F1 progeny | This paper | N/A |
| Oligonucleotides | ||
| Klf16_sgRNA 1: CGTAAGAACAAGCCAAACGGAGG | Sigma | N/A |
| Klf16_sgRNA 2: ATCCATAGCCCGATGGCCGCAGG | Sigma | N/A |
| Maz_sgRNA 1: TCTTGGGGGTCTCGCGCTCGGGG | Sigma | N/A |
| Maz_sgRNA 2: AGGGCCCAATAGGGGATCGCAGG | Sigma | N/A |
| Sp1_sgRNA 1: GAACAGCCAATTACGCGCCGAGG | Sigma | N/A |
| Sp1_sgRNA 2: AAGTAACATCGGTATTCACAAGG | Sigma | N/A |
| Zbtb7a_sgRNA 1: AAGTACGGTTCAATCGGGCGTGG | Sigma | N/A |
| Zbtb7a_sgRNA 2: TAGGGGGCCTTAGCCTATCCAGG | Sigma | N/A |
| Klf16_screen F: AGTGCCTGAATGTGGAGTGGGAG | Sigma | N/A |
| Klf16_screen R: CTACTGTAGACTCTCCTGAGACCTTCC | Sigma | N/A |
| Maz_screen F: AATAAACCACTGGAATGGGGAGG | Sigma | N/A |
| Maz_screen R: AGTACCTATAGGGAGAAACACCAAGG | Sigma | N/A |
| Sp1_screen F: CTCTGACACTTGTGGAGGGCTC | Sigma | N/A |
| Sp1_screen R: ACCAGCAGAAGGCAGGTAAATC | Sigma | N/A |
| Zbtb7a_screen F: CATCTTCTTGGCTAGTGTCACTGC | Sigma | N/A |
| Zbtb7a_screen R: GTGGCAGTCACCTGTGAATAGAC | Sigma | N/A |
| Recombinant DNA | ||
| pSpCas9(BB)-2A-GFP (PX458) | Addgene | Cat #48138 |
| pMy-BirA-T2A-mOrange | Nakahashi et al. 2013 | N/A |
| pMy-BirA-T2A-eGFP | Nakahashi et al. 2013 | N/A |
| pMy-Biotag-SMAD3-T2A-mOrange | This paper | N/A |
| pMy-Biotag-SMAD7-T2A-mOrange | This paper | N/A |
| pMy-Biotag-ZBTB7A-T2A-eGFP | This paper | N/A |
| pMy-Biotag-KLF13-P2A-eGFP | This paper | N/A |
| pMy-PAX5-Biotag-T2A-mOrange | This paper | N/A |
| pCR-Blunt II-Topo-halotag-Smad3 | This paper | N/A |
| pCR-Blunt II-Topo-halotag-Smad7 | This paper | N/A |
| Software and algorithms | ||
| sgRNA CRISPR Design software | https://crispr.zhaopage.com | N/A |
| bowtie2 | Version 2.3.4.1, http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | N/A |
| SAMtools | Version 1.9, http://www.htslib.org/ | N/A |
| bedtools | Version 2.29, https://github.com/arq5x/bedtools2 | N/A |
| UCSC utilities | http://hgdownload.soe.ucsc.edu/admin/exe/ | N/A |
| MACS2 | https://github.com/macs3-project/MACS | N/A |
| DESeq2 | Version 1.22.2, https://bioconductor.org/packages/release/bioc/html/DESeq2.html | N/A |
| STAR | Version 020201, https://github.com/alexdobin/STAR | N/A |
| RSEM | Version 1.3.0, https://deweylab.github.io/RSEM/ | N/A |
| MEME/FIMO | Version 5.0, https://meme-suite.org/meme/doc/download.html | N/A |
| RGT-Hint | https://www.regulatory-genomics.org/hint/introduction/ | N/A |
| Other | ||
| Publicly Available Data Analyzed | Please refer to Suppl. Table 1H for accession numbers of published data analyzed. | N/A |