KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-RelA | Santa Cruz Biotechnology | sc-372; RRID: AB_632037 |
| Goat polyclonal anti-RelA | Santa Cruz Biotechnology | sc-372G; RRID: AB_632037 |
| Rabbit polyclonal anti-RelA | Santa Cruz Biotechnology | cat# sc-109; RRID:AB_632039 |
| Rabbit polyclonal anti-IκBα | Santa Cruz Biotechnology | cat# sc-371; RRID:AB_2235952 |
| Rabbit polyclonal anti-IκBβ | Santa Cruz Biotechnology | cat# sc-945; RRID:AB_631696 |
| Rabbit anti-p50 serum | BioBharati LifeScience (BBL), Kolkata, India | Cat#BB-AB0080 |
| Mouse monoclonal anti-tubulin | Santa Cruz Biotechnology | cat#sc-5286; RRID:AB_628411 |
| Goat polyclonal anti-Actin | Santa Cruz Biotechnology | cat# sc-1615; RRID:AB_630835 |
| Rabbit polyclonal anti-Histone 3 | Abcam | cat# ab1791; RRID:AB_302613 |
| Rabbit monoclonal anti-p84 | Abcam | cat# ab131268; RRID:AB_11156907 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| LPS | Sigma, B5:055 | cat# L2880 |
| Murine TNF | R&D Systems | cat# 410-MT |
| Murine IL-1β | R&D Systems | cat# 401-ML-CF |
| L-Glutamine | Corning | cat# 25–005-CI |
| Penicillin-Streptomycin Solution | Corning | cat# 30002CI |
| β-mercaptoethanol | ThermoFisher | cat# 21985023 |
| Poly(deoxyinosinic-deoxycytidylic) | Sigma-Aldrich | cat# P4929 |
| PEI (polyethylenimine) | Polysciences | cat# #23966–2 |
| Polybrene | Santa Cruz Biotechnology | cat# 134220 |
| Blasticidin | InvioGen | cat# ant-bl |
| Puromycin | InvioGen | cat# ant-pr |
| PMSF (Phenylmethylsulfonyl fluoride) | Sigma-Aldrich | cat# P7626 |
| DTT (Dithiothreitol) | Fisher Scientific | cat# BP172–5 |
| methanol-free Formaldehye solution | ThermoFisher Scientific | cat# 28908 |
| DSG (disuccinimidyl glutarate) | ThermoFisher Scientific | cat# 20593 |
| EDTA-free protease inhibitors | ThermoFisher Scientific | cat# 78439 |
| Proteinase K | Sigma-Aldrich | cat# P2308 |
| PureLink Rnase A | ThermoFisher Scientific | cat# 12091–021 |
| TRIzol | ThermoFisher Scientific | cat# 15596026 |
| Prestained Protein marker | BioPioneer | cat# P-001M |
| Critical Commercial Assays | ||
| Agilent QuikChange II Site-Directed Mutagenesis Kit | Agilent Technologies | cat# 200523 |
| RNeasy Mini Kit | QIAGEN | cat# 74104 |
| Direct-zol RNA Microprep Kit | Zymo Research | cat# R2060 |
| mRNA-seq Library Kit | Kapa Biosystems | cat# KK8421 |
| RNA-seq Library Kit With RiboErase | Kapa Biosystems | cat# KK8483 |
| NEBNEXT Ultra DNA Library Prep Kit for Illumina | New England BioLabs | cat# E7370L |
| dsDNA BR assay Kit | ThermoFisher Scientific | cat# Q32853 |
| dsDNA HS assay Kit | ThermoFisher Scientific | cat# Q32854 |
| AMPure XP beads | Beckman Coulter | cat A63881 |
| Dynabeads Protein G | ThermoFisher Scientific | cat# 1004D |
| SuperSignal West Pico PLUS Chemiluminescent substrate | ThermoFisher Scientific | cat# 34578 |
| SuperSignal West Femto Maximum Sensitivity Substrate | ThermoFisher Scientific | cat# 34095 |
| Deposited Data | ||
| Reference SuperSeries for all sequencing data in this study | NCBI Gene Expression Omnibus | GEO: GSE132540 |
| Experimental Models: Cell Lines | ||
| primary mouse embryonic fibroblasts (MEFs) | This study | N/A |
| Platinum-E (Plat-E) cells | (Morita et al., 2000) | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6: All murine embryonic friboblasts | This study | N/A |
| Mouse: C57BL/6: WT and RelATA/TA | This study | N/A |
| Oligonucleotides | ||
| NF-Y EMSA probe (5′-GAIIIIIICCIGAIIGGIIAAA-3′; 5′-ACTTTTAACCAATCAGGAAAAA-3′) | This Lab and this study | N/A |
| κB EMSA probe (5′-GCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGG-3′) | This Lab and this study | N/A |
| Recombinant DNA | ||
| pBABE-puro vector plasmid DNA | (Morgenstern and Land, 1990) | Morgenstern and Land (Addgene plasmid #1764; RRID:Addgene_1764) |
| Software and Algorithms | ||
| Epoch Spectrophotometer System | Biotek | N/A |
| Qubit 2.0 fluorometer | ThermoFisher Scientific | N/A |
| ImageQuant TL v8.1 | GE Healthcate | N/A |
| Image Lab v6.0 | Bio-Rad | N/A |
| ImageJ v1.50i | NIH, USA | N/A |
| ChemiDoc XRS+ Imaging System | Bio-Rad | N/A |
| Amersham Typhoon Scanner | GE Healthcare | N/A |
| Mathworks MATLAB | MathWorks, Inc. | R2014a |
| ChIPseeker v1.18.0 | (Yu etal., 2015) | N/A |
| deepTools2 | (Ramirez et al., 2016) | N/A |
| HOMER | (Heinz et al., 2010) | N/A |
| Enrichr | (Chen et al., 2013; Kuleshov etal., 2016) | N/A |
| IGV (Integrated Genomics Viewer) | (Robinson et al., 2011) | N/A |
| R(v3.6.1) | N/A | http://www.r-project.org/ |
| Wilcox.test function | R program | N/A |
| mean and standard deviation | Microsoft Excel | N/A |