KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| MIB-1/Ki-67 | Dako | GA626 |
| L1CAM | Sigma | UJ127.11 |
| GFAP | Dako | GA524 |
| EMA | Leica | GP1.4 |
| GFP | Abcam | ab6556 |
| H3K36me3 | Abcam | ab9050 |
| Biological Samples | ||
| Anaplastic ependymoma samples | UCSF Brain Tumor Center | N/A |
| Critical Commercial Assays | ||
| TruSeq RNA Library Prep Kit v2 | Illumina | RS-122- 2001 |
| Nimblegen SeqCap EZ Human Exome Kit v3.0 | Roche | 06465684001 |
| CellTiter 96 Non-Radioactive Cell Proliferation Assay | Promega | G4000 |
| Deposited Data | ||
| DNA Methylation Array | This paper | GEO: GSE142320 |
| RNA-seq data | This paper | SRA: PRJNA597052 |
| WES data | This paper | SRA: PRJNA597052 |
| Experimental Models: Cell Lines | ||
| Human: SF11435 ependymoma cell culture | UCSF Clinical Cancer Genomics Laboratory | SF11435 |
| Oligonucleotides | ||
| G-blocks | IDT | N/A |
| Genotyping: SETD2 forward 5′-TGTAAAACGACGG CCAGTCCTGTTACTCCTCGCGCCG-3′ | This paper | N/A |
| Genotyping: SETD2 reverse 5′-CAGGAAACAGCTA TGACCGGTCAAGCCAACAGCTGCAA-3′). | This paper | N/A |
| SETD2 L1962P correction forward: 5′-GACGCTGA AATAGAGCCCAAAGAGAGCAACGGC-3′ | This paper | N/A |
| SETD2 L1962P correction reverse: 5′-GCCGTTGC TCTCTTTGGGCTCTATTTCAGCGTC-3′ | This paper | N/A |
| SETD2 K2R mutagenesis forward: 5′-TCCGCTAGCG CCACCATGAGGCAGCTGCAGCCGCAGCCGCCTCC-3′ | This paper | N/A |
| SETD2 K2R mutagenesis reverse: 5′-GGAGGCGGCT GCGGCTGCAGCTGCCTCATGGTGGCGCTAGCGGA-3′ | This paper | N/A |
| Recombinant DNA | ||
| SETD2-EGFP | This paper | N/A |
| SETD2K2R-EGFP | This paper | N/A |
| C11orf95 | BACPAC Resources | CH17–67K13; CH17–388O01 |
| RELA | BACPAC Resources | RP11–642F7; CH17–211O12 |
| YAP1 | BACPAC Resources | RP11–11N20; RP11–1082I13 |
| Software and Algorithms | ||
| 3D Slicer v4.8.0 | https://www.slicer.org | https://www.slicer.org |
| R v3.4.3 | https://www.r-project.org | https://www.r-project.org |
| oro.dicom v0.5.3 | Whitcher et al., 2011 | https://cran.r-project.org/web/packages/oro.dicom |
| Kallisto v0.43.1 | Bray et al., 2016 | https://pachterlab.github.io/kallisto/ |
| JAFFA v1.09 | Davidson et al., 2015 | https://github.com/Oshlack/JAFFA/ |
| Tophat v2.1.0 | Kim et al., 2013 | http://ccb.jhu.edu/software/tophat/ |
| Minfi v1.30.0 | Aryee et al., 2014; Fortin et al., 2017 | https://bioconductor.org/packages/release/bioc/html/minfi.html |
| Limma v3.40.0 | Ritchie et al., 2015 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| Conumee v1.3.0 | https://bioconductor.org/packages/release/bioc/html/conumee.html | https://bioconductor.org/packages/release/bioc/html/conumee.html |
| Bcbio | https://github.com/bcbio/bcbio-nextgen | https://github.com/bcbio/bcbio-nextgen |
| Picard suite | http://broadinstitute.github.io/picard | http://broadinstitute.github.io/picard |
| Genome Analysis Toolkit | McKenna et al., 2010 | https://software.broadinstitute.org/gatk/ |
| Varscan2 v2.4.0 | Koboldt et al., 2012 | http://dkoboldt.github.io/varscan/ |
| Freebayes | Garrison and Marth, 2012 | https://github.com/ekg/freebayes |
| Vardict | Lai et al., 2016 | https://github.com/AstraZeneca-NGS/VarDict |
| Snpeff v4.3 | Cingolani et al., 2012 | http://snpeff.sourceforge.net |
| Sequenza v2.1.0 | Favero et al., 2015 | https://cran.r-project.org/web/packages/sequenza/index.html |
| Ape v5.0 | https://cran.r-project.org/web/packages/ape | https://cran.r-project.org/web/packages/ape |