Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (Homo sapiens) |
HEK293F with a stable reporter | PMID:29559556 | ||
| Cell line (Homo sapiens) | HEK293F with a stable reporter, TET1 KO | PMID:30824537 | ||
| Cell line (Homo sapiens) | HEK293F with a stable reporter, TET2 KO | PMID:30824537 | ||
| Cell line (Homo sapiens) | HEK293F with a stable reporter, TET3 KO | PMID:30824537 | ||
| Cell line (Homo sapiens) | HEK293F with a stable reporter, TET TKO | PMID:30824537 | ||
| Cell line (Homo sapiens) | HEK293F with a stable reporter, RELA KO | PMID:30824537 | ||
| Cell line (Homo sapiens) | HEK293F with a stable reporter, MER11B-left KO | This paper | Available upon request | |
| Cell line (Homo sapiens) | HEK293F with a stable reporter, MER11B-right KO | This paper | Available upon request | |
| Cell line (Homo sapiens) | HEK293F with a stable reporter, MER11B-left+right KO | This paper | Available upon request | |
| Cell line (Homo sapiens) | HEK293F with a stable reporter, ERV KO | This paper | Available upon request | |
| Antibody | Rabbit anti-NF-κB p65 |
Santa Cruz | Cat# sc-372; RRID:AB_632037 | 6 μL/ChIP |
| Antibody | Rabbit anti-H3K27ac |
Active Motif | Cat# 39133; RRID:AB_2561016 | 2 μL/ChIP |
| Recombinant DNA reagent | lentiCRISPR v2 | Addgene | Cat# 52961 | |
| Peptide, recombinant protein | Recombinant human TNF-α | Peprotech | Cat# 300-01A | |
| Commercial assay or kit | KAPA HiFi Hotstart Uracil+ ReadyMix PCR kit | Kapa Biosystems | Cat# KK2801 | |
| Commercial assay or kit | CGRP (human) ELISA Kit | Cayman Chemical | Cat# 589101 | |
| Commercial assay or kit | EpiTect Bisulfite Kit | Qiagen | Cat# 59104 | |
| Commercial assay or kit | NEBNext Enzymatic Methyl-seq Conversion Module | NEB | Cat# E7125L | |
| Software, algorithm | BiQ Analyzer | Bock et al., 2005 | version 2.00 | |
| Software, algorithm | FlowJo | Becton, Dickinson and Company | version 7.6.1 | |
| Software, algorithm | GraphPad Prism | GraphPad Software, La Jolla California USA | version 7.00 | |
| Software, algorithm | Bismark v0.22.3 | Krueger and Andrews, 2011; https://github.com/FelixKrueger/Bismark | PMID:21493656 | |
| Software, algorithm | Bowtie2 v2.3.5.1 | http://bowtie-bio.sourceforge.net/bowtie2/ | PMID:22388286 | |
| Software, algorithm | IGV v2.7.2 | http://software.broadinstitute.org/software/igv/ | PMID:21221095 | |
| Software, algorithm | Bedtools | Quinlan laboratory at the University of Utah | PMID:20110278 | |
| Software, algorithm | R software v3.6.0 | https://www.r-project.org/ | The R Foundation | |
| Software, algorithm | Rstudio v1.2.5042 | https://rstudio.com/ | Rstudio Software | |
| Software, algorithm | FastQC v0.11.9 | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | Simon Andrews | |
| Software, algorithm | Cuffdiff v2.2.1 | Trapnell et al., 2012; http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/ | PMID:22383036 | |
| Software, algorithm | STAR v2.7.3a | Dobin et al., 2013; https://github.com/alexdobin/STAR | PMID:23104886 | |
| Software, algorithm | DSS v2.34.0 | https://bioconductor.org/packages/DSS/ | PMID:26819470 | |
| Software, algorithm | deepTools v3.4.2 | Ramírez et al., 2016; https://github.com/deeptools/deepTools | PMID:27079975 | |
| Software, algorithm | Perl v5.26.2 | https://www.perl.org/ | Perl-5.26.2 |