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Ludwig Center for Cancer Genetics and Therapeutics at Johns Hopkins

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Ken Kinzler
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This DAC controls 18 datasets

Dataset ID	Description	Technology	Samples
EGAD00001002263	This is the first dataset for the Botseq sequencing project	Illumina HiSeq 2000 Illumina HiSeq 2500	39
EGAD00001003323	Runs that contain data for the sensitivity and specificity experiments for BiSeqS.	Illumina MiSeq	2
EGAD00001003579	Samples prepared using Safe-SeqS technology. All samples ran on an Illumina MiSeq instrument. Fastq files for read 1 and the index read present (R and I respectively).	Illumina MiSeq	49
EGAD00001003931	Sequencing data from 1,005 cancer patients and 812 healthy controls. All samples prepared using Safe-SeqS technology and sequenced on an Illumina MiSeq and/or HiSeq instrument. Paired FASTQ files for correspond to read 1 and the index read present (R and I respectively).	Illumina HiSeq 4000	212
EGAD00001003958	Whole exome sequencing data for 18 mucoepidermoid carcinoma samples. The samples were used for Illumina TruSeq library construction and captured using Agilent V4 exome panel. The PE fastq files are provided.	Illumina HiSeq 2000	18
EGAD00001003959	Whole genome sequencing data for 25 adenoid cystic carcinoma samples. The samples were used for Illumina TruSeq library construction and were sequenced on an Illumina HiSeq 2000. The PE fastq files are provided.	Illumina HiSeq 2000	25
EGAD00001004355	This dataset consists on 22 samples linked to 22 bam files from whole genome and whole exome sequencing of Esthioneuroblastomas.	Illumina HiSeq 2500	22
EGAD00001004399	ctDNA and protein markers for earlier detection of pancreatic cancers	Illumina HiSeq 4000	14
EGAD00001004946	Whole exome sequencing data for 18 mucoepidermoid carcinoma samples. The samples were used for Illumina TruSeq library construction and captured using Agilent V4 exome panel. The PE fastq files are provided.	Illumina HiSeq 2000	18
EGAD00001004964	Whole exome sequencing data for matched normal and endometriosis samples. Samples were prepared using Agilent Sureselect capture kit, and sequenced on an Illumina HiSeq 2500. The submitted files are in BAM format.	Illumina HiSeq 2500	50
EGAD00001008192	Samples prepared using TruSeq Stranded Total RNA library kit. Samples sequenced on a HiSeq 2000.	Illumina HiSeq 2000	32
EGAD00001008559	Libraries were prepared from RNA-extracted cell lines using Illumina RNA library prep kit. Samples were sequenced on Illumina HiSeq 4000 or HiSeq 2500.	Illumina HiSeq 2500 Illumina HiSeq 4000	103
EGAD00001009757	Bam files aligned using hg19. Sequencing data generated with Illumina MiSeq, HiSeq 2500, or HiSeq 4000 instruments.	Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina MiSeq	62
EGAD00001015410	Paired-end fastq files from whole genome sequencing on Illumina HiSeq 4000 generated using bcl2fastq.	Illumina HiSeq 4000	21
EGAD00001015515	WGS bam files for paired diagnostic and remission samples	Illumina NovaSeq 6000	30
EGAD00001015603	Bam files are from matched normal + "very early" plasma (diagnostic) samples, sequenced on Illumina NovaSeq 6000 instrument. After bwa alignment, duplicates were removed by picard markduplicate, and base quality scores recalibrated using gatk baserecalibrator + apply bqsr.	Illumina NovaSeq 6000	14
EGAD00001015645	Detection of human brain cancers using genomic and immune cell characterization of cerebrospinal fluid through CSF-BAM	Illumina NovaSeq 6000	754
EGAD50000000013	Dataset contains text files that describe the chromosome, position, and read count for an amplicon using the RealSeqS assay.	Illumina HiSeq 4000	150