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Folders and files
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The files: - reads_1.fq.gz - reads_2.fq.gz contain a small selection of short reads from: [1] SRR1548811 dataset (sample replicate 2, concentration log10 (pMol) = -8,57); SRA database http://www.ncbi.nlm.nih.gov/sra/?term=SRR1548811 article: W.B. Tembe et al., Open-access synthetic spike-in mRNA-seq data for cancer gene fusions, BMC Genomics 2014, and [2] RT-4 bladder cell line from Cancer Cell Line Encyclopedia, https://gdc-portal.nci.nih.gov/legacy-archive/files/dc45e1c0-e048-40b5-b48c-8caf3a7bc5ad [3] EOL-1 acute myeloid leukemia cell line from Cancer Cell Line Encyclopedia, https://gdc-portal.nci.nih.gov/legacy-archive/files/f8df0beb-ac7f-450f-aa61-eef082f642ae [4] U-118MG glioblastoma cell line from Cancer Cell Line Encyclopedia, https://gdc-portal.nci.nih.gov/legacy-archive/files/2c1a4f66-567b-46e0-9849-a869ac47ffc2 [5] Homo sapiens isolate case 2 IGH (D2-21)/MALT1 reciprocal breakpoint junction genomic sequence, Accession GQ406059, http://www.ncbi.nlm.nih.gov/nuccore/GQ406059 [6] MUTZ-5 pre-B cell acute lymphoblastic leukemia cell line from Cancer Cell Line Encyclopedia, https://gdc-portal.nci.nih.gov/legacy-archive/files/b82fb337-1b52-4146-b3a8-7878422a8027 [7] NALM-6 pre-B cell acute lymphoblastic leukemia cell line from Cancer Cell Line Encyclopedia, https://gdc-portal.nci.nih.gov/legacy-archive/files/6fa77b04-bb16-49c5-8033-79dd76860c97 [8] SU-DHL-1 anaplastic large cell lymphoma cell line from Cancer Cell Line Encyclopedia, https://gdc-portal.nci.nih.gov/legacy-archive/files/d6f97294-6cdd-4343-b40d-8277df996576 [9] Homo sapiens capicua-like protein/double homeodomain 4 fusion protein (CIC/DUX4 fusion) mRNA, complete cds, Accession DQ388764, https://www.ncbi.nlm.nih.gov/nuccore/DQ388764.1 These short reads were selected manually such that they cover 17 already known fusion genes, which are: - FGFR3-TACC3 (short reads from [2]), - FIP1L1-PDGFRA (short reads from [3]), - GOPC-ROS1 (short reads from [4]), - EWS-ATF1 (short reads from [1]), - TMPRSS2-ETV1 (short reads from [1]), - EWS-FLI1 (short reads from [1]), - NTRK3-ETV6 (short reads from [1]), - CD74-ROS1 (short reads from [1]), - HOOK3-RET (short reads from [1]), - EML4-ALK (short reads from [1]), - AKAP9-BRAF (short reads from [1]), - BRD4-NUT (short reads from [1]), - MALT1-IGH (short reads from [5]), - IGH-CRLF2 (short reads from [6]), - DUX4-IGH (short reads from [7]), - NPM1-ALK (short reads from [8]), and - CIC-DUX4 (short reads from [9]).