{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2500;ILLUMINA"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001003769"],"sample_count":["8"],"description":["EGA dataset EGAD00001003769"],"repository":["EGA"],"title":["Evolution and clinical impact of genetic epistasis within EGFR-mutant lung cancers: multi-timepoint exome sequencing of a single patient's disease"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"description_synonyms":["DER/faint little ball, Ribonucleic, Bru, bar-h1, Raw, PreP, fond, leg, Elp-B1, der, Elp-1, bar, 114 细胞, 114, Errb1, Xkl-1, Tumor, CycEI, AA410010, Bar H1, Long Term, PIG61, l(1)AA33, KL receptor activity, BETA2AR, Gsfsco1, anon-WO0134654.19, Ccne, DmelCG4637, primary tumour, epidermal growth factor-activated receptor activity, AI552599, SCO5, Pop, HRR-1, 1, 2, Barh1, Whole Transcriptome, Transcriptome Sequencing, SCO1, Mir, d-egf-r, Gsfsow3, Effect, Gsfsco5, Non Polyadenylated, RNA Gene Products, SOW3, Svc, thymus nucleic acid, me75, Complete Exome Sequencing, Whole Transcriptome Sequencing, Tissue, DmelCG13969, nucleic acid library preparation, Statistic, W, D17Mit170, flb, T1, NICR1847, l(1)B2/13.1, RUN, Run, PrEP, Bs, 9030024J15Rik, D-EGFR, Malignancies, Double-Stranded DNA, deoxyribonucleic acids, DNAn, Sl, RIP14, Long-Term Effects, NISBD2, DER1, Tumors, B2AR, l(1)LB9, Elp, HRR1, Data Set, Wa5, l(2)09261, ribose nucleic acid, rip14, DEgfr, average., Exome, ribonucleic acids, Longterm Effect, Tr-kit, Double-Stranded, Tl3, Cyc E, br37, Tl2, CG10079, AA33, CG4637, non-small cell lung cancer, (Deoxyribonucleotide)n+m, PBT, MP-1, torpedo/egfr, Benign, BG:DS07108.3, wa2, BH1, ADRBR, Ribonukleinsaeure, bar3, kl1-A, pentosenucleic acids, simple tissue, Ribonucleic acids, median, KIT, hrr1, desoxyribose nucleic acid, l(2)05206, non-small cell lung carcinoma (disease), END, burst, egfr, tyrosine-protein kinase Kit, Acid, pbt, Complete Transcriptome, HD-33, El, l(3)neo56, l(3)neo57, DER/EGFR, EGFR, EGfr, EgfR, dEgfr, Exomes, DER flb, Benign Neoplasms, AI047692, kit, mKIAA1104, Torpedo/Egfr, study protocol, Degfr, Malignant Neoplasms, non-small cell carcinoma of lung, l35Dd, Patient, primary tumor, DEGFR, l(2)57DEFa, l(2)05351, ds DNA, Whole Exome Sequencing, MP1, dEGFR, DmHD-33, DNA, other neoplasm, Transcriptome Sequencings, PEP, krk1, hg, HH, whole exome, CG1849, D-Egf, DNS, cycline, (Deoxyribonucleotide)n, Effects, Complete Exome, non-small cell lung carcinoma, C-erb, Neoplasms, DmcyclinE, Benign Neoplasm, mor1, SCF receptor activity, cycE, non-small cell carcinoma of the lung, mENA, EK2-6, Malignant, aligned, l(2)br37, CG5529, dacer, Deoxyribonucleic acids, CYCLE, Buffer, Hh, cdi7, non-small cell cancer of the lung, method, RNF47, cyclinE, Bar-H1, Deoxyribonucleic Acid, scfr, method used in an experiment, c-erbB, EGFr, Egfr, Gene Products, Cdi7, CDI7, torpedo/Egfr, EGF receptor activity, TOP, Egf-r, NSCLC - non-small cell lung cancer, Low, Del(8)44H, 114 cell, SCFR, CG13969, EGF-R, WES, Fdc, Complete, anatomical systems, Exome Sequencings, CYCE, Malignancy, Longterm, DmelCG3938, CyclE, Mrt, Runt, nucleic acid library construction, 3938, top, Double Stranded, Torpedo/DER, Deoxyribonucleic acid, Long-Term, DmcycE, Sequencing, top/flb, Non-Polyadenylated RNA, Neoplasias, l(2)k05007, NSCLC, dm-cycE, Whole Exome, xfor, l(2)57EFa, bar-3, Clients, Whole, Long-Term Effect, l(2)57Ea, (Deoxyribonucleotide)m, HHT1, LB5, Cancer, Elp-B1RB1, proto-oncogene c-Kit, RNA, l(3)hh, Malignant Neoplasm, Complete Exome Sequencings, cou, Edg, TGF-alpha receptor activity, ERBB, dEGFR1, DNAn+1, barh1, D10Wsu136e, DmelCG1849, aligned to, RNS, Rnt, buffer, Client, lLB5, hrr-1, Exome Sequencing, Lr, l(2)k02514, epidermal growth factor receptor activity, DmCycE, DmelCG5529, DmelCG10079, KIT ligand receptor activity, yeast nucleic acid, Long Term Effects, barH1, Neoplasm, CyeE, DER/top, Non-small cell lung cancer, ds-DNA, Library, XKrk1, FXR, ribonucleic acid, c-KIT, Complete Transcriptome Sequencing, l(2)k02602, Col4a-1, top/DER, primary neoplasia, library construction, Non Polyadenylated RNA, Ntup1, l(2)35Dd, Non-Polyadenylated, 2310012C15Rik, ERBB1, patient, l(1)19Ea, Cancers, Ribonucleic Acid, wa-2, CD117, Longterm Effects, plan specification, fxr, P235, D-CycE, Egf, c-kit, EFG-R, C-Kit, anon-WO0182946.19, Errp, Erbb, Ssm, 38B.6, Der, DER, Desoxyribonukleinsaeure, xkl-1, Bra, Bar, BAR, transforming growth factor-alpha receptor activity, PE, non-small cell cancer of lung, AI450383, ORW1, CG3938, BarHI, DER/torpedo, Neoplasia, ADRB2R, HER1"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-FCI-30-09-2017-16:00:17:587-92 - samples","description":"This dataset is a time-series of EGFR-mutant NSCLC clinical specimens from an individual patient profiled using tumor-based whole exome sequencing and the data is in BAM format. \nDNA was extracted from FFPE for primary tumor and frozen tumor tissue samples and matched non-tumor tissue using the Qiagen Allprep DNA/RNA Mini Kit.  The library preparation protocol was based on the Agilent SureSelect Library Prep and Capture System. DNA was resuspended in a low TE buffer and sheared (Duty Cycle 5%; Intensity 175; Cycles/Burst: 200; Time: 300s, Corvaris S2 Utrasonicator).  Bar-coded exome libraries were prepared using the Agilent Sure Select V5 library kit per manfucaturer’s specifications. The libraries were run on the HiSeq2500.\nRaw paired end reads (100bp) in FastQ format generated by the Illumina pipeline were aligned to the full hg19 genomic assembly obtained from USCS, gencode 14, using bwa version 0.7.12. Picard tools version 1.117 was used to sort, remove duplicate reads and generate QC statistics. Tumor DNA was sequenced to median depth of 303X (range 114.39-383.41) and the matched germline DNA to average depth of 231.65.","dates":{"updated":"2020-07-16 15:33:08"},"accession":"EGAD00001003769","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAC00001000711","EGAS00001002604"]}}