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We present FLASH-seq (FS), a full-length single-cell RNA sequencing (scRNA-seq) method with increased sensitivity and reduced hands-on time compared to Smart-seq3. The entire FS protocol can be performed in ~4.5 hours, is simple to automate and can be easily miniaturized to decrease resource consumption. The FS protocol can also use unique molecular identifiers (UMIs) for molecule counting while displaying reduced strand-invasion artifacts. FS will be especially useful for characterizing gene expression at high resolution across multiple samples.
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http://dx.doi.org/10.1038/s41587-022-01312-3 | DOI Listing |
Bioinformatics
September 2025
Institutional Research Core Program-Biological Data Science Core, University of Alabama at Birmingham, Birmingham, AL United States.
Motivation: Recent advancements in long-read single-cell RNA sequencing (scRNA-seq) have facilitated the quantification of full-length transcripts and isoforms at the single-cell level. Historically, long-read data would need to be complemented with short-read single-cell data in order to overcome the higher sequencing errors to correctly identify cellular barcodes and unique molecular identifiers. Improvements in Oxford Nanopore sequencing, and development of novel computational methods have removed this requirement.
View Article and Find Full Text PDFCell
August 2025
State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen 518083, China; Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Ta
Performing total RNA profiling on formalin-fixed, paraffin-embedded (FFPE) samples, the predominant sample conservation method in clinical practice, remains challenging for current spatial transcriptomics techniques. Here, we introduce Stereo-seq V2, which employs random primers to capture and sequence RNAs in situ on FFPE sections and provides single-cell resolution. The random-priming-based strategy offers unbiased transcript capturing and uniform gene body coverage, which increase the sensitivity to marker genes, the efficiency of non-polyadenylation (poly(A)) RNA profiling, and immune repertoire coverage.
View Article and Find Full Text PDFBioinform Adv
July 2025
IDLab, Department of Information Technology, Ghent University-imec, 9052 Ghent, Belgium.
Motivation: Smart-seq3 is a powerful full-length single-cell RNA sequencing protocol that enables transcript-level quantification and splicing analysis by preserving unique molecular identifier (UMI) information. However, benchmarking computational tools for isoform reconstruction and splicing quantification remains challenging due to the lack of ground truth datasets. Herein, we present smartSim, a Smart-seq3 read simulator designed to generate realistic sequencing data that accurately reflects the complexities of single-cell transcriptomics.
View Article and Find Full Text PDFCrit Rev Oncol Hematol
August 2025
Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai 200433, China. Electronic address:
Extrachromosomal DNA (ecDNA) is a large (typically >5 kb), functional, circular double-stranded DNA molecule that exists independently of chromosomes within the cell nucleus. Its widespread presence in human tumors and crucial role in tumorigenesis have garnered notable attention. Critically, in cancer, they often carry full-length oncogenes along with their regulatory elements.
View Article and Find Full Text PDFPLoS Negl Trop Dis
August 2025
College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.
Balantioides coli is a zoonotic ciliated protozoan that infects humans and other mammals. Conventional and ITS-based genotyping approaches have limitations that hinder precise molecular epidemiological investigations. The objective of this study was to develop a new β-tubulin gene-based approach to enhance the detection and genotyping of B.
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