Project description:Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.
Project description:Single-cell multi-omics sequencing can integrate transcriptome and epigenome to analyze the complex mechanisms underlying neuron development and regeneration, but most current methods are based on second-generation short-read sequencing, which has low efficiency in detecting RNA structural heterogeneity. Long-length sequencing can analyze RNA structures, but the throughput and the number of transcripts detected at the single-cell level are very low, and single-cell level epigenome profiling has not been accomplished either. Therefore, there is currently a lack of an effective method that can integrate RNA splicing and epigenetic modification to analyze the molecular mechanism of neural development. This study developed a single-cell multi-omics assay based on short-read sequencing for the simultaneous detection of single-cell full-length RNA isoforms and DNA accessibility. The accuracy of its resolution in RNA transcript structure can reach 94.5%, and the sensitivity of detecting single-cell gene expression is twice that of third-generation sequencing. And it can detect over 10,000 single nuclei at one run, enabling the effective integrated analysis of single-cell RNA isoforms and DNA accessibility at high throughput. We used this method to construct a multidimensional cell atlas of human retinal organoids, and found that gene expression and differential choices of isoforms of multiple fate-determining factors were significantly associated with chromatin accessibility. This method provides a new technical method for dissecting the multidimensional molecular mechanism of fate determination in neural cell development and regeneration.
2024-07-13 | GSE251754 | GEO
Project description:DNA barcoding of fungal specimens using PacBio long-read high-throughput sequencing
Project description:We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).
Project description:We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).
Project description:We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).
Project description:We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).
Project description:We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).
Project description:The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation including alternative transcription start sites (TSS) and/or alternative internal exon usage. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells.
2021-03-12 | GSE168776 | GEO
Project description:Pocillopora species delimitation
