Targeted bisulfite sequencing in PTC [ATAC-Seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1092043 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28462244_1.fastq.gz | Fastqsanger.gz | |||
| SRR28462244_2.fastq.gz | Fastqsanger.gz | |||
| SRR28462245_1.fastq.gz | Fastqsanger.gz | |||
| SRR28462245_2.fastq.gz | Fastqsanger.gz | |||
| SRR28462246_1.fastq.gz | Fastqsanger.gz |
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Project description:Targeted bisulfite sequencing in PTC
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Project description:This study illuminates the critical advancement in the personalized management of papillary thyroid cancer (PTC) through the identification and validation of epigenetic biomarkers. We discovered the two distinct PTC subgroups with varying prognoses through TBS and observed the clues that PTC1 may related to immune signatures through multi-omics sequencing analysis. Then, we introduce FNAB, a minimally invasive preoperative test, for prognostication and therapeutic decision-making. Utilizing FNAB coupled with real-time digital PCR, our methodology not only facilitates the sensitive detection of seven pivotal biomarkers, but also integrates seamlessly with the established TNM staging system to significantly refine survival predictions. This approach heralds a new era in the precise, personalized treatment of PTC, promising improved patient outcomes through the strategic application of epigenetic insights in clinical practice.
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Project description:This study illuminates the critical advancement in the personalized management of papillary thyroid cancer (PTC) through the identification and validation of epigenetic biomarkers. We discovered the two distinct PTC subgroups with varying prognoses through TBS and observed the clues that PTC1 may related to immune signatures through multi-omics sequencing analysis. Then, we introduce FNAB, a minimally invasive preoperative test, for prognostication and therapeutic decision-making. Utilizing FNAB coupled with real-time digital PCR, our methodology not only facilitates the sensitive detection of seven pivotal biomarkers, including CD37, but also integrates seamlessly with the established TNM staging system to significantly refine survival predictions. This approach heralds a new era in the precise, personalized treatment of PTC, promising improved patient outcomes through the strategic application of epigenetic insights in clinical practice.
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Project description:We present a novel method, termed BisPCR2, for targeted bisulfite sequencing and apply it in the setting of validating type 2 diabetes CpG susceptibility loci
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Project description:We use NGS to assess the ability of TALE-guided DNA methyltranferases to make targeted changes to DNA methylation Targeted bisulfite sequencing of cells infected with wild-type or mutant TALE-DNMT constructs directed to the CDKN2A (p16) locus
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Project description:targeted bisulfite sequencing
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Project description:We applied the solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of 1 million CpGs in more than 21,408 CGIs and 15,946 transcriptional regulatory regions. More than 85% of capture probes successfully yielded quantitative DNA methylation information of targeted regions. In this study, we generated genome-wide, single-base resolution DNA methylation maps in three of the most commonly used breast cancer cell lines.Differentially methylated regions (DMRs) were identified in the 5?-end regulatory regions, as well as the intra- and intergenic regions, particularly in the X chromosome among the three cell lines. The single CpG resolution methylation maps of many known tumor suppressor genes were also established in the three cell lines. Here we present a novel approach that combines solution-phase hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in targeted CGI and promoter regions. We designed 51,466 single strand DNA oligonucleotides (160-mer) which target 23,441 CGIs and the transcription start sites of 19,369 known genes in the human genome. The synthetic long DNA oligonucleotides were converted into biotinylated RNA probes for solution-phase hybridization capture of target DNA. The captured genomic DNA was treated with sodium bisulfite, amplified by PCR and sequenced using Illumina GA IIx sequencer.
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Project description:We report a method for specific capture of an arbitrary subset of genomic targets for single molecule bisulfite sequencing, and for digital quantitation of DNA methylation at a single nucleotide resolution. We used targeted bisulfite sequencing to characterize the changes of DNA methylation during the de-differentiation of human fibroblasts into hybrid stem cells, and into induced pluripotent stem cells. We compared the methylation level of approximately 66,000 CpG sites within 2020 CpG islands on chromosome 12, chromosome 20, and 34 selected regions. A total of 288 differentially methylated regions were identified between fibroblasts and pluripotent cells. Methylation cluster analysis revealed distinct methylation patterns between fibroblasts and pluripotent cells. Furthermore iPS cells are globally more methylated than human embryonic stem cells, which could be due to the reprogramming process. This targeted bisulfite sequencing method is particularly useful for efficient and large-scale analysis of DNA methylation in organisms with large genomes. Experiment Overall Design: Comparison of DNA methylation on 2020 CpG islands and 34 other selected regions among eleven human ES, iPS and fibroblast lines.
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Project description:Targeted bisulfite sequencing (TBS) to study methylation patterns in the conifer species Norway spruce (Picea abies)
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