DAC

The Chinese University of Hong Kong (CUHK) Circulating Nucleic Acids Research Group (CNARG)

Dac ID Contact Person Email Access Information
EGAC00001000078 Peiyong Jiang jiangpeiyong [at] cuhk [dot] edu [dot] hk No additional information is available

This DAC controls 25 datasets:

Dataset ID Description Technology Samples
EGAD00001000284 Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing Illumina Genome Analyzer IIx 1
EGAD00001000290 Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing Illumina Genome Analyzer IIx 1
EGAD00001000308 Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing 1
EGAD00001000395 Noninvasive Prenatal Molecular Karyotyping from Maternal Plasma 1
EGAD00001000856 NA Illumina HiSeq 2000 1
EGAD00001001093 Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing Illumina HiSeq 2000 2
EGAD00001001275 NA Illumina HiSeq 2000 1
EGAD00001001602 NA Illumina HiSeq 2000 1
EGAD00001001609 Maternal Plasma RNA Sequencing for Genomewide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts 14
EGAD00001003705 10 single-cell placental RNA libraries were generated using the Chromium Single Cell 3′ Reagent Kit (10X Genomics). All single-cell libraries were sequenced with a customized paired end with dual indexing (98/14/8/10-bp) format according to the recommendation by 10X Genomics. The data were aligned using the Cell Ranger Single-Cell Software Suite (version 1.0). Moreover, plasma RNA from 22 samples were extracted using the RNeasy Mini Kit (Qiagen). cDNA reverse transcription, second-strand synthesis, and RNA-sequencing (RNA-seq) library construction were performed using the Ovation RNA-seq System V2 (NuGEN) kit according to the manufacturer’s protocol. For alignment of the plasma RNA library, adaptor sequences and low-quality bases on the fragment ends (i.e., quality score < 5) were trimmed, and reads were aligned to the human reference genome (hg19) using the TopHat (v2.0.4) software. All aligned reads were deposited in bam file format. Illumina HiSeq 2000,NextSeq 500 32
EGAD00001003778 NA Illumina HiSeq 2000 1
EGAD00001004204 We used targeted sequencing to capture and measure the abundance as well as the size profiles of EBV DNA in plasma of subjects with and without NPC Illumina HiSeq 2500,NextSeq 500 337
EGAD00001004291 We performed ATAC-seq experiments using 2 placental samples and 2 buffycoat samples. Illumina HiSeq 2500 4
EGAD00001004324 This dataset consist on 70 maternal plasma samples (bam files) used in the FetalQuantSD. The maternal plasma DNA samples were sequenced using the HiSeq 2000 platform (Illumina) with a 50-cycle paired-end mode. Illumina HiSeq 2000 70
EGAD00001004561 Plasma DNA libraries were constructed from 4 mL of plasma without library enrichment, namely without PCR amplification. Paired-end massively parallel sequencing was performed Illumina HiSeq 2000 169
EGAD00001004568 We performed whole genome bisulfite sequencing of plasma DNA in 11 colorectal cancer patients to study the colonic DNA in plasma. Illumina HiSeq 2500 17
EGAD00001004590 DNA-seq from plasma of 14 liver transplantation patients Illumina HiSeq 4000 14
EGAD00001005071 We showed that mice in which Dnase1l3 had been deleted showed aberrations in the fragmentation of plasma DNA. We also observed a change in the ranked frequencies of end motifs of plasma DNA caused by the Dnase1l3 deletion. NextSeq 500 41
EGAD00001005088 NA NextSeq 500 236
EGAD00001005093 NA Illumina HiSeq 4000 118
EGAD00001005286 We developed a new bioinformatics method for detecting the eccDNA in plasma. We revealed that the biological properties between eccDNA and linear DNA are different. eccDNA could be potentially provided as a new class of circulating biomarker. Illumina HiSeq 1500,Illumina HiSeq 2500 15
EGAD00001005371 The biology of cell-free DNA fragmentation and the roles of DNASE1, DNASE1L3 and DFFB NextSeq 500 40
EGAD00001006054 Data were generated by next-generation sequencing (Illumina) in a fastq format. This dataset involved sequencing data from pregnant women and patients with hepatocellular carcinoma (HCC). For HCC samples, the paired buffy coat and tumor DNA tissue samples were also sequenced. Illumina HiSeq 4000 29
EGAD00001006215 Human dnase1l3 deficiency-Mouse AAV samples NextSeq 500 5
EGAD00001006216 Plasma DNA profile in DNASE1L3 deficiency NextSeq 500,Sequel 37