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CUHK Liver Cancer Project DAC

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natwong@cuhk.edu.hk

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This DAC controls 11 datasets

Dataset ID	Description	Technology	Samples
EGAD00001004326	This dataset includes transcriptome sequencing of 17 paired NAFLD-HCC samples and adjacent normal tissues. All the experiments were performed on Illumina HiSeq 2000 platform with raw reads stored in fastq format.	Illumina HiSeq 2000	34
EGAD00001004475	PacBio sequencing data of HKCI-2, HKCI-C1, HKCI-C2, HKCI-C3, HKCI-4, HKCI-9, HKCI-11, HKCI-5A and MIHA. All the data (9 samples) were saved in pacbio hdf5 format.	PacBio RS	9
EGAD00001004476	RNA sequence data for HKCI-2, HKCI-C1, HKCI-C2, HKCI-C3 and MIHA. RNA-seq data of all the 5 samples were stored in compressed fastq format.	Illumina HiSeq 2000	5
EGAD00001005449	This dataset includes ChIP-seq data from two cell lines (HKCI-11 (GOFp53) and MIHA(WT p53)). All the experiments were performed on Illumina HiSeq 2000 platform with raw reads stored in fastq format.	Illumina HiSeq 2000	2
EGAD00001005450	This dataset contains target capture sequence data from 255 samples, including 154 tumors and 101 normal samples. All the experiments were performed on Illumina HiSeq 2000 platform with raw reads stored in fastq format.	Illumina HiSeq 2000	255
EGAD00001005451	This dataset contains whole genome sequence data from 24 samples, including 16 tumors and 8 normal samples. All the experiments were performed on Illumina HiSeq 2000 platform with raw reads stored in fastq format.	Illumina HiSeq 2000	24
EGAD00001005452	This dataset contains whole genome sequence data from 12 samples from 1 patient, including 8 tumor sectors and 4 normal samples. All the experiments were performed on Illumina HiSeq platform with raw reads stored in fastq format.	Illumina HiSeq 2000	12
EGAD00001005453	This dataset contains whole exome sequence data from 86 samples from 6 patient. All the experiments were performed on Illumina HiSeq platform with raw reads stored in fastq format.	Illumina HiSeq 2000	86
EGAD00001015543	H3K4me3, IgG, and Input ChIP-seq in overexpression of pLV Control, CS-FL and CS-ΔEx4 in SW1116 cells	Illumina HiSeq 2000	6
EGAD50000001240	DNA sequencing of sgRNAs in CRISPR-Cas9 screening and RNA sequencing of SF3B4-overexpressing liver organoids	Illumina NovaSeq 6000 Illumina NovaSeq X Sequel II	18
EGAD50000001625	The dataset contains 18 samples. It includs 12 paired whole genome sequencing, and 2 matched short read and long read RNA sequencing of liver organoids, 2 paired RIP RNA sequencing samples. All the experiments were performed on Illumina platform with raw reads stored in fastq format or bam format.	Illumina NovaSeq 6000 Illumina NovaSeq X	18