KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| GAPDH (6C5) | GeneTex, Inc. | GTX28245 RRID:AB_370675 |
| MHC Class I (F-3) | Santa Cruz Biotechnology | sc-55582 RRID:AB_831547 |
| FITC anti-human HLA-A,B,C (W6/32) | BioLegend | 311404 RRID:AB_314873 |
| ZSCAN4 | Invitrogen | PA5–32106 RRID:AB_2549579 |
| DUX4 (14–3) | Geng et al., 2011 | N/A |
| Peroxidase AffiniPure Goat Anti-Mouse IgG (H+L) | Jackson ImmunoResearch | 115–035-146 RRID:AB_2307392 |
| Peroxidase AffiniPure Goat Anti-Rabbit (H+L) | Jackson ImmunoResearch | 111–035-144 RRID:AB_2307391 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Insulin | Sigma-Aldrich | I1882 |
| Recombinant human basic fibroblast growth factor | Promega | G5071 |
| Dexamethasone | Sigma-Aldrich | D4902 |
| Puromycin dihydrochloride | Sigma-Aldrich | P8833 |
| Doxycycline hyclate | Sigma-Aldrich | D9891 |
| Recombinant human IFN-gamma | R&D Systems | 285IF100 |
| Polybrene | Sigma-Aldrich | 107689 |
| Penicillin/streptomycin | Gibco/Thermo Fisher | 15140122 |
| Sodium Pyruvate | Gibco/Thermo Fisher | 11360070 |
| DNase I | Gibco/Thermo Fisher | 18068015 |
| MEM Non-Essential Amino Acids Solution | Gibco/Thermo Fisher | 11140050 |
| Critical Commercial Assays | ||
| Lipofectamine RNAiMAX | Life Technologies | 13778150 |
| SuperScriptIII First-Strand System | Life Technologies | 18080051 |
| iTaq SYBR Green Supermix | Bio-Rad | 1725124 |
| TruSeq RNA Library Preparation Kit | Illumina | RS-122–2001 |
| NucleoSpin RNA kit | Machery-Nagel | 740955 |
| Key Instruments | ||
| QuantStudio 7 Flex | Applied Biosystems | N/A |
| 4200 TapeStation System | Agilent Technologies | N/A |
| Trinean DropSense 96 UV-Vis spectrophotometer | Caliper Life Sciences | N/A |
| Qubit 2.0 Fluorometer | Life Technologies | N/A |
| HiSeq 2500 | Illumina | N/A |
| LSRFortessa X-50 | BD Biosciences | N/A |
| Source Data | ||
| The Cancer Genome Atlas RNA-seq data | CGHub RRID:SCR_002657 | N/A |
| RNA-seq data for Eidahl et al., 2016; Hendrickson et al., 2017; Hugo et al., 2016 | NCBI Gene Expression Omnibus RRID:SCR_005012 | GSE85632, GSE85935, GSE78220 |
| RNA-seq data for Rickard et al., 2015 | NCBI Sequence Read Archive RRID:SCR_004891 | SRP058319 |
| RNA-seq data for Van Allen et al., 2015 | dbGaP RRID:SCR_002709 | phs000452.v2.p1 |
| RNA-seq data for Yasuda et al., 2016 | Japanese Genotype-Phenotype Archive RRID:SCR_003118 | JGAS00000000047 |
| RNA-seq data for Lilljebjörn et al., 2016 | European Genome-phenome Archive RRID:SCR_004944 | EGAD00001002112 |
| GTEx Sample Annotations and Gene Expression | GTEx portal RRID:SCR_013042 | www.gtexportal.org |
| ChIP-seq data for Geng et al., 2012 | NCBI Gene Expression Omnibus RRID:SCR_005012 | GSE33838 |
| Deposited Data | ||
| RNA-seq data for this study | NCBI Gene Expression Omnibus RRID:SCR_005012 | GSE128917 |
| Experimental Models: Cell Lines | ||
| MB135 cells (female) | Snider et al., 2010 | N/A |
| MB2401 cells (male) | Campbell et al., 2018 | N/A |
| MB073 cells (male) | Campbell et al., 2018 | N/A |
| A204 cells (female) | ATCC | HTB-82 RRID:CVCL_1058 |
| HeLa cells (female) | ATCC | CCL-2 RRID:CVCL_0030 |
| MCF-7 cells (female) | ATCC | HTB-22 RRID:CVCL_0031 |
| Mel375 cells (female) and Mel526 cells (unknown) | Dr. Seth Pollack (Pollack et al., 2012) | N/A |
| SuSa cells (male) | DSMZ | ACC 747 RRID:CVCL_L280 |
| MB135iDUX4 cells (female) | Jagannathan et al., 2016 | N/A |
| MB135iDUXB cells (female) | This study | N/A |
| A204iDUX4 cells (female) | This study | N/A |
| HeLaiDUX4 cells (female) | This study | N/A |
| MCF-7iDUX4 cells (female) | This study | N/A |
| Mel375iDUX4 cells (female) | This study | N/A |
| Mel526iDUX4 cells (unknown) | This study | N/A |
| SuSaiDUX4 cells (male) | This study | N/A |
| Oligonucleotides | ||
| Primers for qPCR and cloning See STAR★Methods for sequences |
This study | N/A |
| FlexiTube GeneSolution siRNAs targeting PRPF8 See STAR★Methods for sequences | Qiagen | GS10594 |
| Non-targeting Negative Control siRNA See STAR★Methods for sequence |
Qiagen | 1022076 |
| Recombinant DNA | ||
| pCW57.1 | Addgene | 41397 RRID:Addgene_41397 |
| pCW57.1-DUX4-CA | Addgene | 99281 RRID:Addgene_99281 |
| pCW57.1-DUXB-CA | This study, available on Addgene | 125027 RRID:Addgene_125027 |
| Software and Algorithms | ||
| Bowtie v1.0.0 |
Langmead et al, 2009 RRID:SCR_005476 |
github.com/BenLangmead/bowtie/ |
| RSEM v.1.2.4 | Li and Dewey, 2011 RRID:SCR_013027 | deweylab.github.io/RSEM/ |
| TopHat v2.0.8b | Trapnell et al, 2009 RRID:SCR_013035 | ccb.jhu.edu/software/tophat/index.shtml |
| MISO v2.0 |
Katz et al., 2010 RRID:SCR_003124 |
genes.mit.edu/burgelab/miso/ |
| Samtools v1.3.1 |
Li et al., 2009 RRID:SCR_002105 |
www.htslib.org |
| Kallisto v0.43.0 | Bray et al., 2016 RRID:SCR_016582 | pachterlab.github.io/kallisto/ |
| MACS v2.1.1.20160309 | Zhang et al., 2008 RRID:SCR_013291 | github.com/taoliu/MACS/ |
| IGV v2.3.90 | Thorvaldsdottir et al., 2013 RRID:SCR_011793 | software.broadinstitute.org/software/igv/ |
| Bioconductor |
Huber et al., 2015 RRID:SCR_006442 |
www.bioconductor.org |
| GOseq |
Young et al., 2010 RRID:SCR_017052 |
bioconductor.org/packages/release/bioc/html/goseq.html |
| dplyr | Wickham and Francois RRID:SCR_016708 |
cran.r-project.org/web/packages/dplyr/index.html |
| ggplot2 | Wickham et al., 2009 RRID:SCR_014601 | ggplot2.org |
| GraphPad Prism v7.0 | RRID:SCR_002798 | www.graphpad.com |
| FlowJo v10.5.3 | RRID:SCR_008520 | www.flowjo.com/solutions/flowjo |
| BD FACSDiva | RRID:SCR_001456 | www.bdbiosciences.com/instruments/software/facsdiva/index.jsp |