RNA sequencing protocols

Ebook "Circular RNAs: Methods and protocols" provides established approaches for identifying, characterizing, and manipulating circRNAs in vitro, in vivo, and in silico. Chapters highlight the breakthroughs and the challenges in this new field of research. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

223p lucchinguyen 28-12-2023 3 2   Download

Ebook "RNA detection: Methods and protocols" introduces different concepts and methods of detecting RNA in biological material in a variety of model systems. The chapters in this book discuss methods that will answer numerous biological questions that arise in the study of RNAs. Some of the topics covered in this book are single mRNA molecule detection in embryos and neurons; detection of mRNA and associated molecules by ISH-IEM on frozen sections; optimizing molecular beacons for intracellular analysis of RNA;...

492p lucchinguyen 28-12-2023 6 2   Download

Ebook "Epstein barr virus: Methods and protocols" explores data from the applications of molecular biological methods and the applications of recent immunological and cytogenetic methods in Epstein-Barr Virus (EBV) that will offer readers possible new solutions to the unresolved problems in the EBV field. Chapters in this book cover topics such as: viral life cycle, latency, EBV-associated diseases and EBV diagnostics;...

273p lucchinguyen 28-12-2023 5 2   Download

Ebook "Argonaute proteins: Methods and protocols" aids researchers in examining these versatile proteins in a wide variety of cell types; features practical, step-by-step protocols which open the door to future progress in the field of molecular therapeutics; contains expert tips and vital implementation advice to ensure success;...

262p lucchinguyen 28-12-2023 5 2   Download

Single-cell RNA-seq has emerged as an innovative technology used to study complex tissues and characterize cell types, states, and lineages at a single-cell level. Classification of bulk tumors by their individual cel‑ lular constituents has also created new opportunities to generate single-cell atlases for many organs, cancers, and developmental models.

16p visharma 20-10-2023 4 2   Download

Part 1 book "RT-PCR Protocols" includes content: Single cell RT-PCR on mouse embryos - A general approach for developmental biology; detection of influenza a virus neuraminidase and pb2 gene segments by one step reverse transcription polymerase chain reaction; RT-PCR amplification and cloning of large viral sequences,... and other contens.

189p oursky05 20-09-2023 1 0   Download

Single-cell RNA-seq technologies require library preparation prior to sequencing. Here, we present the first report to compare the cheaper BGISEQ-500 platform to the Illumina HiSeq platform for scRNA-seq. We generate a resource of 468 single cells and 1297 matched single cDNA samples, performing SMARTer and Smart-seq2 protocols on two cell lines with RNA spike-ins.

8p vigalileogalilei 27-02-2022 11 1   Download

Droplet-based single-cell RNA sequencing protocols have dramatically increased the throughput of single-cell transcriptomics studies. A key computational challenge when processing these data is to distinguish libraries for real cells from empty droplets.

9p vigalileogalilei 27-02-2022 10 1   Download

We introduce a k-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all k-mers with differential abundance directly from the raw data files.

15p vialfrednobel 29-01-2022 13 0   Download

A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains transcripts in viable single cells, allowing one to disconnect time and place of sampling from subsequent processing steps.

15p vialfrednobel 29-01-2022 6 0   Download

Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid, reproducible results, and a systematic benchmarking is required before entering large-scale data production.

16p viarchimedes 26-01-2022 9 0   Download

An important challenge in pre-processing data from droplet-based single-cell RNA sequencing protocols is distinguishing barcodes associated with real cells from those binding background reads. Existing methods test barcodes individually and consequently do not leverage the strong cell-to-cell correlation present in most datasets.

10p viarchimedes 26-01-2022 8 0   Download

Aneuploidies are copy number variants that affect entire chromosomes. They are seen commonly in cancer, embryonic stem cells, human embryos, and in various trisomic diseases. Aneuploidies frequently affect only a subset of cells in a sample; this is known as “mosaic” aneuploidy. A cell that harbours an aneuploidy exhibits disrupted gene expression patterns which can alter its behaviour. However, detection of aneuploidies using conventional single-cell DNA-sequencing protocols is slow and expensive.

8p vilarryellison 29-10-2021 15 1   Download

Current library preparation protocols for Illumina HiSeq and MiSeq DNA sequencers require ≥2 nM initial library for subsequent loading of denatured cDNA onto flow cells. Such amounts are not always attainable from samples having a relatively low DNA or RNA input; or those for which a limited number of PCR amplification cycles is preferred (less PCR bias and/or more even coverage).

10p vibeauty 23-10-2021 11 1   Download

This inhibits 3′ adapter ligation and makes library preparation particularly challenging. To reduce bias, the NEBNext kit (New England Biolabs) uses polyethylene glycol (PEG), the NEXTflex V2 kit (BIOO Scientific) uses both randomised adapters and PEG, and the novel SMARTer (Clontech) and CATS (Diagenode) kits avoid ligation altogether. Here we compared these methods with Illumina’s classical TruSeq protocol regarding the detection of normal and 2’ OMe RNAs. In addition, we modified the TruSeq and NEXTflex protocols to identify conditions that improve performance.

16p vibeauty 23-10-2021 8 0   Download

Cell type-specific ribosome-pulldown has become an increasingly popular method for analysis of gene expression. It allows for expression analysis from intact tissues and monitoring of protein synthesis in vivo. However, while its utility has been assessed, technical aspects related to sequencing of these samples, often starting with a smaller amount of RNA, have not been reported. In this study, we evaluated the performance of five library prep protocols for ribosome-associated mRNAs when only 250 pg-4 ng of total RNA are used.

16p vitzuyu2711 29-09-2021 13 1   Download

Circulating microRNAs (miRNAs) are attractive non-invasive biomarkers for a variety of conditions due to their stability and altered pathophysiological expression levels. Reliable detection of global expression profiles is required to maximise miRNA biomarker discovery.

12p visilicon2711 20-08-2021 6 1   Download

RNA-Seq is currently the most widely used tool to analyze whole-transcriptome profiles. There are numerous commercial kits available to facilitate preparing RNA-Seq libraries; however, it is still not clear how some of these kits perform in terms of: 1) ribosomal RNA removal; 2) read coverage or recovery of exonic vs. intronic sequences; 3) identification of differentially expressed genes (DEGs); and 4) detection of long non-coding RNA (lncRNA).

20p visilicon2711 20-08-2021 14 1   Download

Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the impact of number of polymerase chain reaction (PCR) steps (1- or 2- steps) and choice of target marker gene region (V3 V4 and V4) on the presentation of the upper and lower airway microbiome.

15p vilichoo2711 25-06-2021 14 1   Download

Adapter trimming is a prerequisite step for analyzing next-generation sequencing (NGS) data when the reads are longer than the target DNA/RNA fragments. Although typically used in small RNA sequencing, adapter trimming is also used widely in other applications, such as genome DNA sequencing and transcriptome RNA/cDNA sequencing, where fragments shorter than a read are sometimes obtained because of the limitations of NGS protocols.

12p vikentucky2711 26-11-2020 10 0   Download