Small RNA sequencing - Wikipedia
Small RNA sequencing (Small RNA-Seq) is a type of RNA sequencing based on the use of NGS technologies that allows to isolate and get information about noncoding RNA molecules in order to evaluate and discover new forms of small RNA and to predict their possible functions.
Small RNA Sequencing | Small RNA and miRNA profiling and
Small RNA sequencing (RNA-Seq) is a technique to isolate and sequence small RNA species, such as microRNAs (miRNAs). Small RNA-Seq can query thousands of small RNA and miRNA sequences with unprecedented sensitivity and dynamic range.
Small-seq for single-cell small-RNA sequencing - Nature
2018年9月24日 · We describe Small-seq, a ligation-based method that enables the capture, sequencing, and molecular counting of small RNAs from individual mammalian cells. Here, we provide a detailed protocol...
COMPSRA: a COMprehensive Platform for Small RNA-Seq data …
2020年3月12日 · We present COMPSRA, a comprehensive modular stand-alone platform for identifying and quantifying small RNAs from small RNA sequencing data. COMPSRA contains prebuilt customizable standard...
SPAR - Sequencing-based Pipeline for Analysis of small RNAs
2018年8月23日 · To get started, select and analyze a reference small RNA-seq dataset from ENCODE and DASHR or analyze your own small RNA dataset by uploading or providing a URL for web-accessible small RNA data. See tutorials for examples on how to use SPAR and prepare your data for analysis.
A Beginner’s Guide to Small RNA Sequencing - Novogene
Small RNA sequencing (sRNA-Seq) serves as a robust research tool with diverse applications: Profiling known and novel sRNA transcripts: Systematic identification and characterization of both established and novel small RNA transcripts within biological samples.
Small RNA Sequencing (sRNA-seq) - Novogene
Small RNAs (sRNAs) are short RNA molecules, usually non-coding, involved with gene silencing and the post-transcriptional regulation of gene expression. sRNA Sequencing (sRNA-seq) is a method that enables the in-depth investigation of these RNAs, in special microRNAs (miRNAs, 18-40nt in length).
DASHR - Database of small human noncoding RNAs
DASHR (Database of small human non-coding RNAs) is a database developed at the University of Pennsylvania with the most comprehensive expression and processing information to date on all major classes of human small non-coding RNA (sncRNA) genes and mature sncNA annotations, expression levels, sequence and RNA processing information across 185 h...
Small RNA-Seq - Strand NGS
Analyze your small RNA data to find expression levels of various small RNA species. Detect novel small RNA genes. Visualize the results in small RNA-specific gene view. Identify targets of miRNAs common to multiple target prediction databases.
Small RNA-Seq - TATAA Biocenter
Small RNA-Seq Sequencing targets small RNA species (typically 18-30 nucleotides), such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs), capturing RNA-mediated gene regulation.
Small-seq for single-cell small-RNA sequencing - PubMed
We describe Small-seq, a ligation-based method that enables the capture, sequencing, and molecular counting of small RNAs from individual mammalian cells. Here, we provide a detailed protocol for this approach that relies on standard reagents and instruments.
Novel small RNA-seq - NEB
We show that a randomized splint ligation-based workflow can reduce bias and increase the sensitivity of small RNA sequencing for a wide variety of small RNAs, including microRNA (miRNA) and tRNA fragments as well as 2’OMe modified RNA, including Piwi-interacting RNA and …
Small RNA-Sequencing: Approaches and Considerations for …
2021年5月27日 · Small RNA-seq enables genome-wide profiling and analysis of known, as well as novel, miRNA variants. Moreover, its high sensitivity allows for profiling of low input samples such as liquid biopsies, which have now found applications in diagnostics and prognostics.
SMARTer smRNA-Seq Kit for Illumina—sequence small RNAs with …
The SMARTer smRNA-Seq Kit for Illumina has been specifically designed to generate high-quality Illumina-ready sequencing libraries from low-input amounts of small RNAs such as these.
sRNAflow: A Tool for the Analysis of Small RNA-Seq Data
2024年1月24日 · The analysis of small RNA sequencing data across a range of biofluids is a significant research area, given the diversity of RNA types that hold potential diagnostic, prognostic, and predictive value.
Small RNA Sequencing: Introduction, Workflow, and Applications
Small RNA sequencing (RNA-Seq) is a method for isolating and sequencing small RNA species such as microRNAs (miRNAs). With unparalleled sensitivity and versatile range, Small RNA-Seq can analyze dozens of small RNA especially miRNA sequences.
Small RNA-seq Data Standards and Processing Pipeline
There are many classes of small RNAs (tRNAs, microRNAs, miRNA, snoRNAs, etc…) less than 200 nucleotides in length, each of which carries out distinct biochemical roles in the cell. These roles may include messenger RNA interference silencing and degredation, among others.
Small RNA Sequencing (sRNA-seq) - CD Genomics
We generate small RNA sequencing libraries directly from total RNA and Capture the complete range of small RNAs, to understand the roles they play. this will provide you with a comprehensive and efficient approach to understand post-transcriptional regulation and …
sRNAflow: A Tool for the Analysis of Small RNA-Seq Data - MDPI
2024年1月17日 · The analysis of small RNA sequencing data across a range of biofluids is a significant research area, given the diversity of RNA types that hold potential diagnostic, prognostic, and predictive value.
Small RNA-Seq for Ribosome Profiling (Ribo-Seq) | Revvity
2024年10月2日 · Ribosome profiling, or Ribo-Seq, has emerged as a powerful technique that provides a snapshot of ribosome positions on messenger RNA (mRNA) transcripts, revealing which genes are being actively translated.
Noncanonical role of ALAS1 as a heme-independent inhibitor of small RNA …
2024年12月19日 · The raw sequencing data for ALAS1-KO Ago2 CLEAR-CLIP, ALAS1-KO HEK293T small RNA-seq, Alas1/2 mouse hepatocyte small RNA, and total RNA-seq were deposited in the National Center for Biotechnology Information Gene Expression Omnibus under accession nos. GSE261576, GSE261577, GSE261600, and GSE273381, respectively.
Scalable and unsupervised discovery from raw sequencing reads …
2024年9月23日 · Fig. 2: SPLASH2 enables rapid de novo discovery of RNA editing in single-cell RNA-seq and alternative splicing in cancer cell lines. Similar content being viewed by others
Secuer: Ultrafast, scalable and accurate clustering of single ... - PLOS
2022年12月5日 · Author summary Recently, single-cell RNA sequencing (scRNA-seq) has enabled profiling of thousands to millions of cells, spurring the development of efficient clustering algorithms for large or ultra-large datasets. In this work, we developed an ultrafast clustering method, Secuer, for small to ultra-large scRNA-seq data. Using simulation and real datasets, …
Stranded, total RNA libraries from low input samples for same-day ...
The SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian (referred to as “Pico v3”) is designed for efficient preparation of sequencing libraries from picogram amounts (10 ng–250 pg) of high- or low-quality total RNA (RIN 2–10, DV200 > 25%). ... The Singular Genomics libraries show a small high molecular weight (HMW) peak ...
Integrating Circle-Seq with transcriptomics reveals genome-wide ...
2024年11月29日 · The circular structure of eccDNAs were confirmed. Integration of Circle-Seq and RNA-Seq data identified that large eccDNAs can be directly transcribed in non-dividing cardiomyocytes, indicating their potential roles in gene expression. Small circular DNA elicited a stronger cytokine response than linear DNA with the same sequence. Conclusions
Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA ...
2015年2月2日 · Differential RNA sequencing (RNA-seq) of wild-type V. cholerae and a locked low-cell-density QS-mutant strain identified 7,240 transcriptional start sites with ∼47% initiated in the antisense direction. A total of 107 of the transcripts do not appear to encode proteins, suggesting they specify regulatory RNAs.
Embracing the dropouts in single-cell RNA-seq analysis
2020年3月3日 · One primary reason that makes single-cell RNA-seq analysis challenging is dropouts, where the data only captures a small fraction of the transcriptome of each cell. Almost all computational ...
C3+ cancer-associated fibroblasts promote tumor growth and …
2024年12月20日 · To further investigate, small interfering RNA (siRNA)-mediated knockdown of C3 in CAFs was employed in vitro, with subsequent experiments, including cell migration assays, cell viability assays, and immunofluorescence, revealing significant functional impacts. ... Infiltration levels of C3 + CAFs in bulk RNA-seq data were estimated by averaging ...
DNA sequencing - Wikipedia
DNA sequencing may be used to determine the sequence of individual genes, larger genetic regions (i.e. clusters of genes or operons), full chromosomes, or entire genomes of any organism. DNA sequencing is also the most efficient way to indirectly sequence RNA or proteins (via their open reading frames).In fact, DNA sequencing has become a key technology in many areas of …
TFAP2A drives non-small cell lung cancer (NSCLC) progression …
2024年12月18日 · Sultana A, Alam MS, Liu X, Sharma R, Singla RK, Gundamaraju R, et al. Single-cell RNA-seq analysis to identify potential biomarkers for diagnosis, and prognosis of non-small cell lung cancer by ...
Cepharanthine as an effective small cell lung cancer inhibitor ...
2024年11月28日 · Background Small cell lung cancer (SCLC) is an aggressive malignancy with limited treatment options and poor prognosis, underscoring the need for new therapeutic agents. ... (RNA-seq) were used to ...
Small extracellular vesicles derived from umbilical cord …
2024年12月20日 · Radiation-induced heart disease (RIHD) is one of the most serious complications of radiation therapy (RT) for thoracic tumors, and new interventions are needed for its prevention and treatment. Small extracellular vesicles (sEVs) from stem cells have attracted much attention due to their ability to repair injury. However, the role of umbilical cord …
NIS-Seq enables cell-type-agnostic optical perturbation screening
2024年12月19日 · a, Genome-wide NIS-Seq perturbation screening in HeLa–Cas9–p65–mNeonGreen cells stimulated with IL-1β.Fold changes are calculated based on the mean pixel-wise Pearson correlation between ...