EGAGenomicsNextSeq 500;ILLUMINAhttps://ega-archive.org/datasets/EGAD00001003986180EGA dataset EGAD00001003986EGAVasp, VASP, DmelCG15112, ENHANCER OF ATNSI ACTIVITY, Data Set, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, 2018., ENA/VASPIPP2A2, chemical properties, determination, Phylogenetic Structure, Phylogenetic Analysis, Xkl-1, Phylogenetic Signals, 5730420M11Rik, KL receptor activity, Gsfsco1, Phylogenetic Inference, dorsal marginal zone, Method, SCO5, Molecular Phylogenetics, Comparative Analysis, SCO1, Analysis, Polymerase Chain, Phylogenetic Comparative Analysis, rounded, Gsfsow3, Gsfsco5, Phylogenetic Relationship, SOW3, Group, SET, Phylogenomic, thymus nucleic acid, TAF-I, Molecular, Inverse Polymerase Chain Reaction, W, Phylogenetic Networks, DmelCG4299, IGAAD, set, DmelCG10574, Phylogenetic Network, scientific observation, Reaction, sample, Phylogenetic Reconstructions, Bs, Phylogenetic Incongruences, s, Double-Stranded DNA, Phylogenetic Clustering, deoxyribonucleic acids, Relationship, DNAn, Sl, phapii, Phylogenetic Comparative Method, Anchored Polymerase Chain Reaction, chemical characterization, Phylogenetic Analyse, StF-IT-1, Tr-kit, Phylogenetic Inferences, Double-Stranded, Phylogenetic Analyses, predicted, Phylogenetic Generalized Least Squares, (Deoxyribonucleotide)n+m, PBT, kl1-A, Henson's node, Phylogenetic Comparative Analyses, KIT, Phylogenetic Incongruence, desoxyribose nucleic acid, END, PCR, tyrosine-protein kinase Kit, pbt, Phylogenetic Tree, HLA-DR-associated protein II, Nested Polymerase Chain Reaction, DI-2, I-2Dm, pooled, Phylogenies, CG4299, kit, chemical content, polymerase chain reaction, experimental procedures, I-2PP1, Phylogenetic Trees, TAF-IBETA, Patient, Comparative Method, Clustering, ds DNA, DMZ, Phylogenetic Groups, TAF-Ibeta, DNA, i2pp2a, Community, krk1, Phylogenetic Reconstruction, DNS, experimental, (Deoxyribonucleotide)n, SCF receptor activity, Polymerase Chain Reactions, Network, Inverse, Distance, PHAPII, Deoxyribonucleic acids, Phylogenomics, gDNA, Inverse PCR, Phylogenetic Comparative Methods, Inference, Deoxyribonucleic Acid, scfr, Relatedness, tumor sample, Phylogenetic Relatednesses, Phylogenetic Relatedness, SCFR, Community Phylogenetics, Fdc, methods, nodus primitivus, experimental section, ipp2a2, Signal, 2pp2a, Double Stranded, Deoxyribonucleic acid, chemical composition., Phylogenetic Distances, Structure, CG10574, Reconstruction, 2PP2A, taf-ibeta, stem node, Clients, dSET, dSet, Phylogenetic Distance, Incongruence, Anchored PCR, (Deoxyribonucleotide)m, chemical structure, HHT1, measuring, Molecular Phylogenetic, proto-oncogene c-Kit, Edg, DNAn+1, igaad, Tree, Phylogenetic Comparative, Client, Phylogenetic Clusterings, group, I-2PP2A, KIT ligand receptor activity, Dm I-2, chemical analysis, I2PP2A, ds-DNA, Library, XKrk1, Anchored, c-KIT, Phylogenetic Group, Reactions, Nested, nodal stem, ensemble, patient, Phylogenetic Signal, Phylogenetic Structures, CD117, sample population, Analyse, dSET/TAF-Ibeta, 2610030F17Rik, c-kit, Phylogenetic, C-Kit, Ssm, Community Phylogenetic, Phylogenetic Relationships, Desoxyribonukleinsaeure, xkl-1, Nested PCR, round, assay, ORW1, AA407739falseena-DATASET-BCCA-26-02-2018-20:05:22:038-668 - samplesA total of 192 positions per patient were deeply sequenced in each corresponding tumor sample (including 4 experimental controls and SNVs predicted to originate at each node of the sample phylogeny, see Zhang et al. for details). Genomic DNA templates were used as starting material to generate PCR products. PCR was set up using Phusion DNA polymerase according to the manufacturer’s specifications. The standard PCR conditions used were an initial denaturation at 98C for 30 seconds, followed by 35 cycles of 98C for 10 seconds, 60C for 15 seconds and 72C for 8 seconds, and a final extension at 72C for 10 minutes. PCR products were cleaned up using PCRClean DX beads. Amplicons were pooled by template for sequencing sample preparation. Sample preparation involved a second round of amplification using Phusion DNA polymerase with 6 PCR cycles, with primers specified in Zhang et al. DNA quality was assessed using the Caliper LabChip GX HighSensitivity Assay and DNA quantity was measured using a Qubit dsDNA HS assay kit on a Qubit fluorometer. The indexed libraries were pooled together and sequenced on the Illumina NextSeq500 platform with paired-end 150bp reads using v2 chemistry reagents.2022-11-22 12:10:03EGAD000010039869606EGAC00000000011EGAS00001002839