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Deep amplicon sequencing to infer malignant clonal populations for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

A 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.

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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00001879750 bam 61.0 MB
EGAF00001879751 bam 62.1 MB
EGAF00001879752 bam 62.9 MB
EGAF00001879753 bam 63.4 MB
EGAF00001879754 bam 45.0 MB
EGAF00001879755 bam 45.7 MB
EGAF00001879756 bam 46.3 MB
EGAF00001879757 bam 46.6 MB
EGAF00001879758 bam 46.9 MB
EGAF00001879759 bam 47.5 MB
EGAF00001879760 bam 48.4 MB
EGAF00001879761 bam 48.6 MB
EGAF00001879762 bam 53.7 MB
EGAF00001879763 bam 54.6 MB
EGAF00001879764 bam 55.3 MB
EGAF00001879765 bam 55.9 MB
EGAF00001879766 bam 39.6 MB
EGAF00001879767 bam 39.9 MB
EGAF00001879768 bam 40.6 MB
EGAF00001879769 bam 40.9 MB
EGAF00001879770 bam 44.7 MB
EGAF00001879771 bam 45.4 MB
EGAF00001879772 bam 45.9 MB
EGAF00001879773 bam 46.4 MB
EGAF00001879774 bam 44.5 MB
EGAF00001879775 bam 45.3 MB
EGAF00001879776 bam 46.0 MB
EGAF00001879777 bam 46.1 MB
EGAF00001879778 bam 47.4 MB
EGAF00001879779 bam 48.1 MB
EGAF00001879780 bam 49.0 MB
EGAF00001879781 bam 49.1 MB
EGAF00001879782 bam 53.0 MB
EGAF00001879783 bam 53.8 MB
EGAF00001879784 bam 54.8 MB
EGAF00001879785 bam 54.9 MB
EGAF00001879786 bam 40.4 MB
EGAF00001879787 bam 41.2 MB
EGAF00001879788 bam 41.7 MB
EGAF00001879789 bam 42.0 MB
EGAF00001879790 bam 44.9 MB
EGAF00001879791 bam 45.7 MB
EGAF00001879792 bam 46.4 MB
EGAF00001879793 bam 46.6 MB
EGAF00001879794 bam 63.3 MB
EGAF00001879795 bam 64.4 MB
EGAF00001879796 bam 65.4 MB
EGAF00001879797 bam 65.7 MB
EGAF00001879798 bam 42.3 MB
EGAF00001879799 bam 42.9 MB
EGAF00001879800 bam 43.7 MB
EGAF00001879801 bam 43.9 MB
EGAF00001879802 bam 32.0 MB
EGAF00001879803 bam 32.5 MB
EGAF00001879804 bam 33.0 MB
EGAF00001879805 bam 33.1 MB
EGAF00001879806 bam 36.2 MB
EGAF00001879807 bam 36.9 MB
EGAF00001879808 bam 37.4 MB
EGAF00001879809 bam 37.7 MB
EGAF00001879810 bam 37.4 MB
EGAF00001879811 bam 37.9 MB
EGAF00001879812 bam 38.5 MB
EGAF00001879813 bam 38.7 MB
EGAF00001879814 bam 27.8 MB
EGAF00001879815 bam 28.4 MB
EGAF00001879816 bam 28.5 MB
EGAF00001879817 bam 29.0 MB
EGAF00001879818 bam 31.9 MB
EGAF00001879819 bam 32.4 MB
EGAF00001879820 bam 32.9 MB
EGAF00001879821 bam 33.1 MB
EGAF00001879822 bam 33.6 MB
EGAF00001879823 bam 34.0 MB
EGAF00001879824 bam 34.6 MB
EGAF00001879825 bam 34.8 MB
EGAF00001879826 bam 33.6 MB
EGAF00001879827 bam 33.9 MB
EGAF00001879828 bam 34.7 MB
EGAF00001879829 bam 34.7 MB
EGAF00001879830 bam 49.8 MB
EGAF00001879831 bam 50.6 MB
EGAF00001879832 bam 51.6 MB
EGAF00001879833 bam 51.8 MB
EGAF00001879834 bam 48.6 MB
EGAF00001879835 bam 49.4 MB
EGAF00001879836 bam 50.2 MB
EGAF00001879837 bam 50.3 MB
EGAF00001879838 bam 29.7 MB
EGAF00001879839 bam 30.2 MB
EGAF00001879840 bam 30.7 MB
EGAF00001879841 bam 30.8 MB
EGAF00001879842 bam 53.6 MB
EGAF00001879843 bam 54.4 MB
EGAF00001879844 bam 55.2 MB
EGAF00001879845 bam 55.6 MB
EGAF00001879846 bam 55.6 MB
EGAF00001879847 bam 56.3 MB
EGAF00001879848 bam 57.6 MB
EGAF00001879849 bam 57.6 MB
EGAF00001879850 bam 37.3 MB
EGAF00001879851 bam 37.8 MB
EGAF00001879852 bam 38.6 MB
EGAF00001879853 bam 38.6 MB
EGAF00001879854 bam 42.2 MB
EGAF00001879855 bam 42.8 MB
EGAF00001879856 bam 43.6 MB
EGAF00001879857 bam 43.8 MB
EGAF00001879858 bam 40.5 MB
EGAF00001879859 bam 41.0 MB
EGAF00001879860 bam 41.9 MB
EGAF00001879861 bam 42.0 MB
EGAF00001879862 bam 35.7 MB
EGAF00001879863 bam 36.4 MB
EGAF00001879864 bam 37.1 MB
EGAF00001879865 bam 37.2 MB
EGAF00001879866 bam 37.4 MB
EGAF00001879867 bam 38.2 MB
EGAF00001879868 bam 38.7 MB
EGAF00001879869 bam 38.9 MB
EGAF00001879870 bam 31.2 MB
EGAF00001879871 bam 31.7 MB
EGAF00001879872 bam 32.2 MB
EGAF00001879873 bam 32.5 MB
EGAF00001879874 bam 50.7 MB
EGAF00001879875 bam 51.7 MB
EGAF00001879876 bam 52.4 MB
EGAF00001879877 bam 52.6 MB
EGAF00001879878 bam 27.9 MB
EGAF00001879879 bam 28.5 MB
EGAF00001879880 bam 29.0 MB
EGAF00001879881 bam 29.0 MB
EGAF00001879882 bam 49.0 MB
EGAF00001879883 bam 49.8 MB
EGAF00001879884 bam 50.6 MB
EGAF00001879885 bam 50.9 MB
EGAF00001879886 bam 37.8 MB
EGAF00001879887 bam 38.5 MB
EGAF00001879888 bam 39.0 MB
EGAF00001879889 bam 39.3 MB
EGAF00001879890 bam 59.3 MB
EGAF00001879891 bam 60.4 MB
EGAF00001879892 bam 61.1 MB
EGAF00001879893 bam 61.9 MB
EGAF00001879894 bam 52.5 MB
EGAF00001879895 bam 53.3 MB
EGAF00001879896 bam 54.3 MB
EGAF00001879897 bam 54.4 MB
EGAF00001879898 bam 44.1 MB
EGAF00001879899 bam 44.8 MB
EGAF00001879900 bam 45.4 MB
EGAF00001879901 bam 45.7 MB
EGAF00001879902 bam 39.9 MB
EGAF00001879903 bam 40.5 MB
EGAF00001879904 bam 41.2 MB
EGAF00001879905 bam 41.4 MB
EGAF00001879906 bam 39.1 MB
EGAF00001879907 bam 39.5 MB
EGAF00001879908 bam 40.3 MB
EGAF00001879909 bam 40.5 MB
EGAF00001879910 bam 42.0 MB
EGAF00001879911 bam 42.5 MB
EGAF00001879912 bam 43.1 MB
EGAF00001879913 bam 43.3 MB
EGAF00001879914 bam 45.4 MB
EGAF00001879915 bam 46.2 MB
EGAF00001879916 bam 46.8 MB
EGAF00001879917 bam 47.2 MB
EGAF00001879918 bam 34.5 MB
EGAF00001879919 bam 35.5 MB
EGAF00001879920 bam 35.6 MB
EGAF00001879921 bam 36.2 MB
EGAF00001879922 bam 33.4 MB
EGAF00001879923 bam 34.1 MB
EGAF00001879924 bam 34.4 MB
EGAF00001879925 bam 34.7 MB
EGAF00001879926 bam 43.3 MB
EGAF00001879927 bam 44.6 MB
EGAF00001879928 bam 44.7 MB
EGAF00001879929 bam 45.4 MB
180 Files (7.8 GB)