Project description:We present scNanoATAC-seq (Single-cell Assay for Transposase Accessible Chromatin by Oxford Nanopore Technologies Sequencing), an effective method for simultaneous detection of chromatin accessibility and genetic variation. Long fragments (about 4-5Kb) of single-cell ATAC-seq library were enriched and sequenced by Oxford Nanopore Technologies platform. Ends of long ATAC-seq fragments are regarded as chromatin accessibility signal in downstream analysis.
Project description:We present scNanoATAC-seq (Single-cell Assay for Transposase Accessible Chromatin by Oxford Nanopore Technologies Sequencing), an effective method for simultaneous detection of chromatin accessibility and genetic variation. Long fragments (about 4-5Kb) of single-cell ATAC-seq library were enriched and sequenced by Oxford Nanopore Technologies platform. Ends of long ATAC-seq fragments are regarded as chromatin accessibility signal in downstream analysis.
Project description:Transposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described to date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions within repeating genomic sequences where the repeat units are longer than the sequence read length. To overcome this limitation, we have developed a TIS method using Oxford Nanopore sequencing technology that generates and uses long nucleotide sequence reads; we have called this method LoRTIS (Long Read Transposon Insertion-site Sequencing). This experiment data contains sequence files generated using Nanopore and Illumina platforms. Biotin1308.fastq.gz and Biotin2508.fastq.gz are fastq files generated from nanopore technology. Rep1-Tn.fastq.gz and Rep1-Tn.fastq.gz are fastq files generated using Illumina platform. In this study, we have compared the efficiency of two methods in identification of transposon insertion sites.
Project description:This study elucidates the molecular mechanisms underlying the antitumor effects of a novel sulfane sulfur donor compound on hepatocellular carcinoma (HCC) cells using RNA sequencing analysis. While sulfane sulfur has emerged as a crucial signaling molecule with therapeutic potential in cancer treatment, its precise mechanisms of action remain to be fully elucidated. We synthesized a novel sulfane sulfur donor (persulfided cysteine precursor, PSCP) that exhibits potent inhibitory effects on HCC cells. Through comprehensive RNA-seq analysis of PSCP-treated HCC cells versus controls, we uncovered a complex regulatory mechanism involving mitochondrial damage, AMPK activation, and p53-mediated cellular responses, including both proliferation inhibition and apoptosis induction. Our findings demonstrate that PSCP exerts its anti-HCC effects through a mitochondrial damage-AMPK-p53 signaling cascade, with p53 serving as a key mediator that both suppresses cell proliferation and promotes apoptosis. These results provide novel insights into the antitumor mechanisms of sulfane sulfur compounds and highlight their therapeutic potential in HCC treatment. Treatment group: SNU398 HCC cells treated with 200 μM PSCP for 24 hours Control group: SNU398 cells treated with vehicle control Three-four biological replicates per group mRNA extraction using TRIzol reagent (Invitrogen, MD, USA) Sequencing performed by Biomarker Technologies (Guangzhou, China) Sequencing platform: Oxford Nanopore Technologies (Oxford, UK) Data analysis conducted using BMK_Cloud platform
Project description:Human cancer cell lines were pulsed with thymidine analogues EdU and BrdU, sequenced on the Oxford Nanopore platform, and analysed with our DNAscent software to measure DNA replication stress.
Project description:The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for clinical sequencing. We recently demonstrated ONT shallow whole-genome sequencing to detect copy number alterations (CNA) from the circulating tumor DNA (ctDNA) of cancer patients. Here, we show that cell-type and cancer-specific methylation changes can also be detected, as well as cancer-associated fragmentation signatures. This feasibility study suggests that ONT shallow WGS could be a powerful tool for liquid biopsy, especially real-time medical applications.