KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| ECL rabbit IgG, HRP-linked whole Ab | GE Health care | Cat#NA934; RRID: AB_772206 |
| ECL mouse IgG, HRP-linked whole Ab | GE Health care | Cat# NA931; RRID: AB_772210 |
| GAPDH (14C10) | Cell Signaling | Cat# 2118S; RRID: AB_561053 |
| alpha tubulin: Alexa Fluor 488 | Invitrogen | Cat#53-4502-82;RRID:AB_1210525 |
| NFkB1 p105/p50 | Cell Signaling | Cat# 3035S; RRID: AB_330564 |
| NFkB p65 | Cell Signaling | Cat# 8242S; RRID: AB_10859369 |
| brachyury | Cell Signaling | Cat# 81694S; RRID: AB_2799983 |
| c-Myc (9E10) | Santa Cruz | Cat# sc-40; RRID: AB_627268 |
| HaloTag | Promega | Cat# G921A; RRID: AB_2688011 |
| HA-tag | Cell Signaling | Cat# 3724S; RRID: AB_1549585 |
| DYKDDDDK Tag | Cell Signaling | Cat# 14793S; RRID: AB_2572291 |
| Bacterial and virus strains | ||
| E. coli BL21-RIPL codon plus | Agilent Technologies | Cat# 230280 |
| NEB 5-alpha | New England BioLabs | Cat# C2987H |
| Rosetta 2 DE3 | Sigma | Cat# 71397 |
| Chemicals, peptides, and recombinant proteins | ||
| Tumor Necrosis Factor-α human recombinant protein | Sigma | Cat# T0157–10UG |
| dCas9 recombinant protein | Crews Lab | N/A |
| Ni-NTA agarose | QIAGEN | Cat# 30250 |
| Cycloheximide | Sigma | Cat# C104450 |
| RNAiMAX transfection reagent | Thermo Fisher Sci | Cat# 13778–150 |
| MLN4924 | selleckchem | Cat# S7109 |
| Janelia Fluor 646 (JF646) HaloTag Ligand | Promega | Cat# ga1120 |
| Critical commercial assays | ||
| High-Capacity cDNA Reverse Transcription Kit | Applied Biosystem | Cat# 4368814 |
| KAPA SYBR FAST qPCR Master Mix Kit | Kapa Biosystems | Cat# KK4600 |
| Experimental models: cell lines | ||
| HEK293T | ATCC | Cat# CRL-3216 |
| Flp-In T-Rex 293 | Thermo Fisher Sci | Cat# R78007 |
| HeLa | ATCC | Cat# CCL-2 |
| Experimental models: organisms/strains | ||
| Zebrafish (Danio rerio) wildtype strain TL | Scott Holley Lab, Yale University | N/A |
| Oligonucleotides | ||
| F_CTdCas9:ACCTGACTATGCTGGAGTG GATAAGAAATACUCAATAGGCTTAGCT ATCGGC | Yale School of Medicine | N/A |
| R_CTdCas9:ATCAGCGGGTTTAACCGGA AATCUCCAGAGTAGACAGCC | Yale School of Medicine | N/A |
| F_CTPCDNA5:AGATTTCCGGTTAAACC CGCTGAUCAGCCTCGAC | Yale School of Medicine | N/A |
| R_CTPCDNA5:AGTATTTCTTATCCACTC CAGCATAGTCAGGUACGTCATAAGGG | Yale School of Medicine | N/A |
| RNA:DNA chimeric oligos | This manuscript | Figure S1 |
| pCDNA5-HA-NTdCas9HT7 | This manuscript | Table S1 |
| pCDNA5-HA-NTdCas9HT7-NLS | This manuscript | Table S1 |
| Recombinant DNA | ||
| pET302-6His-dCas9-Halo | Deng et al Proc Natl Acad. 2015 | Addgene, Cat# 72269 |
| pCDNA5-HA-CTdCas9HT7 | This manuscript | N/A |
| pCDNA5-HA-NTdCas9HT7-NLS | This manuscript | N/A |
| pNL-Flag-Nluc-GFP | This manuscript | N/A |
| TBXTA-c005 | Opher Gileadi SGC expression vectors | Addgene Cat# 139754 |
| Software and algorithms | ||
| Image Lab 6.0 | BioRad | https://www.bio-rad.com/en-us/product/image-lab-software?ID=KRE6P5E8Z |
| Graphpad | Prism | https://www.graphpad.com/scientific-software/prism/ |