Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (H. sapiens) | 1881 myoblasts | Fields Center for FSHD and Neuromuscular Research at the University of Rochester Medical Center (https://www.urmc.rochester.edu/neurology/fields-center.aspx) | See Supplementary file 3 | |
| Cell line (H. sapiens) | 2305 myoblasts | Fields Center for FSHD and Neuromuscular Research at the University of Rochester Medical Center (https://www.urmc.rochester.edu/neurology/fields-center.aspx) | See Supplementary file 3 | |
| Cell line (H. sapiens) | 2338 myoblasts | Fields Center for FSHD and Neuromuscular Research at the University of Rochester Medical Center (https://www.urmc.rochester.edu/neurology/fields-center.aspx) | See Supplementary file 3 | |
| Cell line (H. sapiens) | 2453 myoblasts | Fields Center for FSHD and Neuromuscular Research at the University of Rochester Medical Center (https://www.urmc.rochester.edu/neurology/fields-center.aspx) | See Supplementary file 3 | |
| Cell line (H. sapiens) | 54–2 myoblasts | (Krom et al., 2012) (DOI:10.1016/j.ajpath.2012.07.007) | See Supplementary file 3 | |
| Cell line (H. sapiens) | eMHF2 iPS cells | University of Washington Institute for Stem Cell and Regenerative Medicine Tom and Sue Ellison Stem Cell Core (http://depts.washington.edu/iscrm/ellison) | ||
| Cell line (H. sapiens) | HFF3 fibroblasts | ATCC | ATCC:SCRC-1043; RRID:CVCL_DB29 | |
| Cell line (H. sapiens) | MB073 myoblasts | Fields Center for FSHD and Neuromuscular Research at the University of Rochester Medical Center (https://www.urmc.rochester.edu/neurology/fields-center.aspx) | See Supplementary file 3 | |
| Cell line (Homo sapiens) | MB135 myoblasts | Fields Center for FSHD and Neuromuscular Research at the University of Rochester Medical Center (https://www.urmc.rochester.edu/neurology/fields-center.aspx) | See Supplementary file 3 | |
| Cell line (H. sapiens) | MB200 myoblasts | Fields Center for FSHD and Neuromuscular Research at the University of Rochester Medical Center (https://www.urmc.rochester.edu/neurology/fields-center.aspx) | See Supplementary file 3 | |
| Cell line (H. sapiens) | MB2401 myoblasts | Fields Center for FSHD and Neuromuscular Research at the University of Rochester Medical Center (https://www.urmc.rochester.edu/neurology/fields-center.aspx) | See Supplementary file 3 | |
| Antibody | alpha-Tubulin | Sigma-Aldrich | Sigma-Aldrich:T9026; RRID:AB_477593 | |
| Antibody | Acetyl-Histone H4 | EMD Millipore | EMD Millipore:06866; RRID:AB_310270 | |
| Antibody | CHD4 | Bethyl Laboratories | Bethyl Laboratories:A301081A; RRID:AB_873001 | |
| Antibody | DUX4 (14–3) | (Geng et al., 2011) | ||
| Antibody | DUX4 (E5-5) | (Geng et al., 2011) | ||
| Antibody | FITC anti-mouse | Jackson ImmunoResearch | Jackson ImmunoResearch:715095150; RRID:AB_2340792 | |
| Antibody | FLAG M2 | Sigma-Aldrich | Sigma-Aldrich:F1804 or F3165; RRID:AB_262044 or RRID:AB_259529 | |
| Antibody | HDAC2 | Abcam | Abcam:ab7029; RRID:AB_305706 | |
| Antibody | HRP anti-mouse | Jackson ImmunoResearch | Jackson ImmunoResearch:115035146; RRID:AB_2307392 | |
| Antibody | MBD2 | Bethyl Laboratories | Bethyl Laboratories:A301632A; RRID:AB_1211478 | |
| Antibody | MTA2 | Abcam | Abcam:ab8106; RRID:AB_306276 | |
| Antibody | TRITC anti-rabbit | Jackson ImmunoResearch | Jackson ImmunoResearch:711025152; RRID:AB_2340588 | |
| Recombinant DNA reagent | pCW57.1-MBD3L2 | This paper | Addgene plasmid #106332 | Lentiviral vector expressing doxycycline-inducible MBD3L2 (generated using pCW57.1 [Addgene plasmid #41393]) |
| Recombinant DNA reagent | pGIPZ-shControl | Fred Hutchinson Cancer Research Center Genomics Shared Resource (http://monod.fhcrc.org/rnai/) | ||
| Recombinant DNA reagent | pGIPZ-shMBD3L-1 | Fred Hutchinson Cancer Research Center Genomics Shared Resource (http://monod.fhcrc.org/rnai/) | ||
| Recombinant DNA reagent | pGIPZ-shMBD3L-2 | Fred Hutchinson Cancer Research Center Genomics Shared Resource (http://monod.fhcrc.org/rnai/) | ||
| Recombinant DNA reagent | pZLCv2-3xFLAG-dCas9-HA-2xNLS | This paper | Addgene plasmid #106357 | Lentiviral vector expressing FLAG-tagged, nuclease-deficient Cas9 (generated using lentiCRISPRv2 [Addgene plasmid #52961] and pHR-SFFV-KRAB-dCas9-P2A-mCherry [Addgene plasmid #60954]) |
| Recombinant DNA reagent | pZLCv2-gD4Z4-1-3xFLAG-dCas9-HA-2xNLS | This paper | Addgene plasmid #106352 | Lentiviral vector expressing FLAG-dCas9 and a guide RNA targeting the D4Z4 unit |
| Recombinant DNA reagent | pZLCv2-gD4Z4-2-3xFLAG-dCas9-HA-2xNLS | This paper | Addgene plasmid #106353 | Lentiviral vector expressing FLAG-dCas9 and a gRNA targeting the D4Z4 unit |
| Recombinant DNA reagent | pZLCv2-gD4Z4-3-3xFLAG-dCas9-HA-2xNLS | This paper | Addgene plasmid #106354 | Lentiviral vector expressing FLAG-dCas9 and a gRNA targeting the D4Z4 unit |
| Recombinant DNA reagent | pZLCv2-gMYOD1-3xFLAG-dCas9-HA-2xNLS | This paper | Addgene plasmid #106355 | Lentiviral vector expressing FLAG-dCas9 and a gRNA targeting the MYOD1 distal regulatory region |
| Sequenced-based reagent | enChIP-/ChIP-qPCR primers | This paper | See Supplementary file 4 | |
| Sequenced-based reagent | gRNAs | This paper | See Supplementary file 4 | |
| Sequenced-based reagent | RT-qPCR primers | This paper | See Supplementary file 4 | |
| Sequenced-based reagent | shRNAs | This paper | See Supplementary file 4 | |
| Sequenced-based reagent | siRNAs | This paper | See Supplementary file 4 | |
| Peptide, recombinant protein | 3X FLAG peptide | Sigma-Aldrich | Sigma-Aldrich:F4799 | |
| Commercial assay or kit | QIAshredder | Qiagen | Qiagen:79656 | |
| Commercial assay or kit | RNeasy Mini Kit | Qiagen | Qiagen:74106 | |
| Commercial assay or kit | SuperScript III First-Strand Synthesis System | Invitrogen/Thermo Fisher | Invitrogen/Thermo Fisher:18080051 | |
| Chemical compound, drug | 2-Mercaptoethanol | Sigma-Aldrich | Sigma-Aldrich:M3148 | |
| Chemical compound, drug | Dexamethasone | Sigma-Aldrich | Sigma-Aldrich:D4902 | |
| Chemical compound, drug | DMEM:Nutrient Mixture F-12 | Gibco/Thermo Fisher | Gibco/Thermo Fisher:11320082 | |
| Chemical compound, drug | DNase I | Thermo Fisher | Thermo Fisher:18068015 | |
| Chemical compound, drug | Doxycyline hyclate | Sigma-Aldrich | Sigma-Aldrich:D9891 | |
| Chemical compound, drug | Dulbecco's Modified Eagle Medium (DMEM) | Gibco/Thermo Fisher | Gibco/Thermo Fisher:11965092 | |
| Chemical compound, drug | Dynabeads-Protein G | Thermo Fisher | Thermo Fisher:10003D | |
| Chemical compound, drug | Ham's F-10 Nutrient Mix | Gibco/Thermo Fisher | Gibco/Thermo Fisher:11550043 | |
| Chemical compound, drug | Horse serum | Gibco/Thermo Fisher | Gibco/Thermo Fisher:26050070 | |
| Chemical compound, drug | HyClone Fetal Bovine Serum | GE Healthcare Life Sciences | GE Healthcare Life Sciences:SH30071.03 | |
| Chemical compound, drug | Insulin | Sigma-Aldrich | Sigma-Aldrich:I1882 | |
| Chemical compound, drug | KnockOut Serum Replacement | Gibco/Thermo Fisher | Gibco/Thermo Fisher:10828028 | |
| Chemical compound, drug | Lipofectamine RNAiMAX | Invitrogen/Thermo Fisher | Invitrogen/Thermo Fisher:13778150 | |
| Chemical compound, drug | Matrigel | Corning Life Science | Corning Life Science:354277 | |
| Chemical compound, drug | MEM non-essential amino acids | Gibco/Thermo Fisher | Gibco/Thermo Fisher:11140050 | |
| Chemical compound, drug | mTeSR1 medium | STEMCELL Technologies | STEMCELL Technologies:85850 | |
| Chemical compound, drug | Opti-MEM reducedserum medium | Thermo Fisher | Thermo Fisher:31985070 | |
| Chemical compound, drug | Penicillin/streptomycin | Gibco/Thermo Fisher | Gibco/Thermo Fisher:15140122 | |
| Chemical compound, drug | Polybrene | Sigma-Aldrich | Sigma-Aldrich:107689 | |
| Chemical compound, drug | Puromycin | Sigma-Aldrich | Sigma-Aldrich:P8833 | |
| Chemical compound, drug | Recominant human basic fibroblast growth factor | Promega Corporation | Promega Corporation:G5071 | |
| Chemical compound, drug | Sodium pyruvate | Gibco/Thermo Fisher | Gibco/Thermo Fisher:11360070 | |
| Chemical compound, drug | Transferrin | Sigma-Aldrich | Sigma-Aldrich:T0665 | |
| Chemical compound, drug | Y-27632 ROCK inhibitor | Miltenyi Biotec | Miltenyi Biotec:130106538 | |
| Software, algorithm | Code used for proteomics data analysis | This paper (Jagannathan, 2017) | The R code used for the proteomics data analysis can be accessed via github at https://github.com/sjaganna/2017-campbell_et_al | |
| Software, algorithm | GraphPad Prism | GraphPad Prism (https://graphpad.com) | RRID:SCR_015807 | Version 6 |
| Software, algorithm | ImageJ | ImageJ (http://imagej.nih.gov/ij/) | RRID:SCR_003070 | |
| Software, algorithm | Proteome Discoverer | Thermo Fisher | RRID:SCR_014477 | Version 1.4 |