Sequencing total RNA

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

Current single-cell RNA-seq approaches are hindered by preamplification bias, loss of strand of origin information, and the inability to observe small-RNA and mRNA dual transcriptomes. Here, we introduce a single-cell holotranscriptome sequencing (Holo-Seq) that overcomes all three hurdles.

22p vigalileogalilei 27-02-2022 8 1   Download

Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction.

10p vibeauty 23-10-2021 6 1   Download

The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides). P. carnosa was grown on each substrate for over one month, and mycelia were harvested at five time points for total RNA sequencing. Residual wood powder was also analyzed for total sugar and lignin composition.

13p vitzuyu2711 29-09-2021 13 1   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

Formalin-fixed and paraffin-embedded (FFPE) blocks held in clinical laboratories are an invaluable resource for clinical research, especially in the era of personalized medicine. It is important to accurately quantitate gene expression with degraded and small amounts of total RNA from FFPE materials.

13p viansan2711 30-07-2021 21 1   Download

RNA sequencing is a powerful approach to quantify the genome-wide distribution of mRNA molecules in a population to gain deeper understanding of cellular functions and phenotypes. However, unlike eukaryotic cells, mRNA sequencing of bacterial samples is more challenging due to the absence of a poly-A tail that typically enables efficient capture and enrichment of mRNA from the abundant rRNA molecules in a cell.

12p vijeeni2711 30-06-2021 20 1   Download

Albino mutations are commonly observed in the animal kingdom, including in bivalves. In the blacklipped pearl oyster Pinctada margaritifera, albino specimens are characterized by total or partial absence of colouration resulting in typical white shell phenotype expression.

13p vijeeni2711 30-06-2021 12 2   Download

There are challenges in generating mRNA-Seq data from whole-blood derived RNA as globin gene and rRNA are frequent contaminants. Given the abundance of erythrocytes in whole blood, globin genes comprise some 80% or more of the total RNA.

9p vilichoo2711 25-06-2021 22 1   Download

MicroRNAs (miRNAs) are highly conserved class of short endogenous non-coding small RNA molecules of about 18–22 nucleotide in length. MicroRNAs negatively regulate the gene expression by degrading target mRNA. In the present study, comparative genomic based approach was used to identify and characterize new conserved microRNAs in “orphan legume crop” pigeon pea (Cajanus cajan L.) using expressed sequence tags (ESTs) by in silico method. A total of 4,621 unique previously reported microRNAs were used for homology search in 25,576 ESTs of pigeon pea for identifying conserved miRNAs.

11p nguaconbaynhay6 24-06-2020 12 2   Download

The 16S rRNA gene is composed of highly conserved, specie-specific sequences between different species of bacteria and the application of restriction endonucleases on the amplified 16S rRNA gene is a novel diagnostic tool in molecular characterization of bacterial isolates.

10p nguaconbaynhay6 23-06-2020 11 0   Download

Light plays an important role in plant growth and development. In this study, the impact of light on physiology of 20-d-old Arabidopsis leaves was examined through transcriptomic, proteomic and metabolomic analysis.

17p vihashirama2711 21-05-2020 12 1   Download

This study compared the performance of five commercially available kits in extracting total RNA from small eukaryotic tissue samples (

13p viuchiha2711 21-04-2020 12 0   Download

Plant Growth Promoting Rhizobacteria (PGPR) are a group of rhizospheric bacteria, found in association with plant roots and enhance the growth of plant directly or indirectly. To isolate multi-trait PGPR, total 7 soil sample were collected from sugarcane rhizosphere with diverse previous cropping pattern. Total 38 distinct isolates were obtained in pure culture from above collected samples, were screened for their ability of plant growth promoting characters in in vitro conditions. Out of this, 100% showed antagonistic potential, 55.26%, 42.11% and 52.

7p chauchaungayxua3 07-02-2020 16 1   Download

Aims of present study were to isolate and characterize chitinase producing fungi from soil samples of apple orchards of Shimla and Kinnaur district of Himachal Pradesh. The soil samples were collected aseptically and subjected to serial dilution to isolate the fungal strains. Total nine morphologically different fungi were isolated and screened for their chitinolytic activity in colloidal chitin incorporated media through zone assay. The isolates were screened based on the size of the zone formed. Best chitinase producers were subjected 18S ribosomal RNA sequencing.

8p nguaconbaynhay1 04-12-2019 26 0   Download

The dysregulation of long non-coding RNAs (lncRNAs) is associated with the development of various diseases. However, little is known about the regulatory function of lncRNAs in peritendinous fibrosis. Therefore, the expression profiles of lncRNAs and mRNAs in normal tendon and fibrotic peritendinous tissues were analyzed in this study using RNA sequencing. In total, 219 lncRNAs and 3403 mRNAs were identified that were differentially expressed between the two sets of tissues.

10p trinhthamhodang1 14-11-2019 12 1   Download

The transcription patterns of 64 linear double stranded DNA templates obtained with T7 RNA polymerase were investigated. These templates consisted of 17 nucleotide-long sequences under the control of the minimal bac-teriophage T7 promoter and represented all possible combinations of nucleotides at positions +8, +10 and +11.

8p tumor12 20-04-2013 30 3   Download

We purified pancreatic deoxyribonuclease I (DNase I) from the shark Heterodontus japonicususing three-step column chromatography. Although its enzymatic properties resem-bled those of other vertebrateDNases I, sharkDNase I was unique inbeingabasicprotein.Full-lengthcDNAs encoding theDNases I of two shark species,H. japonicusandTriakis scyllia, were constructed from their total pancreatic RNAs using RACE.

8p awards 05-04-2013 45 3   Download