Transcriptome amplification analysis. Medical search. Frequent questions

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. (nature.com)
Unbiased amplification of genomic DNA and total RNA or mRNA (poly A+) is achieved using innovative Multiple Displacement Amplification (MDA) technology and the novel REPLI-g SensiPhi DNA Polymerase. (qiagen.com)
cDNA amplified using the REPLI-g Cell WGA & WTA Kit demonstrates a high degree of reproducibility from experiment to experiment, with minimal "technical noise", ensuring highly reliable results (see figure High level of experimental reproducibility and minimized technical noise. Whole transcriptome amplification (WTA) using the REPLI-g Cell WGA & WTA Kit was performed using the mRNA (poly A+) enrichment protocol to reduce rRNA amplification. WTA amplified cDNA was fragmented (Covaris S220) and an NGS sequencing library was prepared using the GeneRead Library Prep I Kit (QIAGEN). Sequencing was done on a MiSeq Instrument (Illumina), RNA biotypes were mapped using Bowtie2, and reads per kilobase and million mapped reads (RPKM) were calculated. Results demonstrate comparable results, with an R 2 value of 0.91, between the RPKM values of one 25-cell sample versus transcripts derived from the average of all WTA samples tested (5 samples of 25, 50, or 100 cells). "> High level of experimental reproducibility and minimized technical noise ). (qiagen.com)
Since the transcriptome includes the transcription of all mRNA in cells, except for abnormal mRNA degradation (like transcriptional decay), the transcriptome reflects the genes that are actively expressed at any given time. (capitalbiotechnology.com)
Isolated mRNA was used for RNAseq analysis and qPCR. (biomedcentral.com)

Following efficient cell lysis, (and complete removal of genomic DNA followed by sensitive reverse transcription for the WTA reaction), the kit utilizes Multiple Displacement Amplification (MDA) technology for complete and unbiased amplification of gDNA and cDNA (see figure Multiple Displacement Amplification (MDA) technology. Primers (arrows) anneal to the template DNA and are extended at 30ºC by REPLI-g SensiPhi DNA polymerase, which moves along the gDNA or cDNA template strand, displacing the complementary strand while becoming a template itself for replication. In contrast to PCR-based amplification, MDA does not require different temperatures and ends in very long fragments with low mutation rates. "> Multiple Displacement Amplification (MDA) technology ). (qiagen.com)
Construction of long-transcript enriched cDNA libraries from submicrogram amounts of total RNAs by a universal PCR amplification method. (nih.gov)
Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. (nih.gov)
The droplets are broken open and the bound RNA reverse-transcribed into cDNA to form barcoded STAMPs (single cell transcriptomes attached to microparticles). (chemyx.com)
c The Ct value and Tm value distribution of 20 % Percoll solution, 10 pg total RNA, non-target well and target well during cDNA amplification process in microwells. (rna-seqblog.com)
Gene specific primers were designed based on the published sequence for Acheta domesticus Apolipophorin III, and PCR amplification was performed to assess the presence of transcripts for Apolipophorin III in the cDNA derived from the tissues. (emerging-researchers.org)
Cycle threshold (CT) values and quantification of ethidium bromide stained PCR amplification product showed no significant differences in levels of apolipophorin transcripts in a subset of cDNA prepared ovaries and DLMs of Day 1 and 3 crickets. (emerging-researchers.org)
Conclusion: We developed a GATC-PCR method to accurately measure absolute expression levels of mRNAs by means of competitive amplification of genomic and cDNA copies of each gene. (elsevierpure.com)

De novo assembly and analysis of the transcriptome of Ocimum americanum var. (biomedcentral.com)
A total of 115,022,842 high quality, clean reads were obtained from four libraries (two replicates of control samples and two replicates of chilling-treated samples) and were used to perform de novo transcriptome assembly. (biomedcentral.com)
The CBF-mediated transcriptional cascade, a well-known cold tolerance pathway, was reconstructed using our de novo assembled transcriptome. (biomedcentral.com)
. pilosum and a de novo assembled transcriptome, which can be used to characterize genes related to diverse biological processes. (biomedcentral.com)
Thus the first Illumina-based de novo transcriptome sequencing and analysis of the chicken parasite Plasmodium gallinaceum was performed to assess the evolution of essential Plasmodium genes. (biomedcentral.com)
This de novo assembly of a red clover transcriptome from leaf material of droughted and non-droughted plants provides a rich source for gene identification, single nucleotide polymorphisms (SNP) and short sequence repeats (SSR). (biomedcentral.com)
Increasing the number of reads should increase the level of uniquely mapped reads to facilitate the de novo assembly and quantification analysis, but this approach can also increase the cost of library preparation and sequencing [ 2 ], which can be wasteful in terms of data storage and processing. (biomedcentral.com)
For an organism that lacks a high-quality reference genome, the de novo assembly of its transcriptome is a useful method for researchers to find the transcripts or genes responsive to various treatments and to better understand the expression patterns of the candidate genes. (biomedcentral.com)
In addition, the de novo assembled transcripts using the default parameters in most current assemblers are usually short in length, which hampers further sequence-based analysis and experiments. (biomedcentral.com)

Novel CIC point mutations and an exon-spanning, homozygous deletion identified in oligodendroglial tumors by a comprehensive genomic approach including transcriptome sequencing. (genomeweb.com)

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. (nature.com)

Four ethylene receptors genes ( AcERS1b , AcERS1b , AcETR2a , and AcETR2b ) have been cloned, and expression analysis showed that AcERS1b , AcETR2a , and AcETR2b play key roles in pineapple flowering 13 . (nature.com)
Expression profiles analysis identifies the values of carcinogenesis and the prognostic prediction of three genes in adrenocortical carcinoma. (cancerindex.org)
Following this, the differentially expressed genes (DEGs) were included in Gene Ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, protein‑protein interaction network and survival analyses. (cancerindex.org)
Moreover, this work highlights the P. gallinaceum transcriptome as an important public resource for investigating the diversity and evolution of essential Plasmodium genes. (biomedcentral.com)
Using transcriptomic analysis in D283-MED cells, we found a large transcriptional remodelling upon long term hypoxia, in particular the expression of a number of genes involved in detection and repair of double strand breaks (DSB) was altered. (biomedcentral.com)
Transcription analysis showed that the expression levels of the HpDGAT2A , HpDGAT2D , and HpDGAT2E genes markedly increased under high light and nitrogen deficient conditions with distinct patterns, which led to significant TAG and EAST accumulation. (researchsquare.com)
The potential signaling pathways for RIL were identified and experimentally validated using gene ontology (GO) enrichment and Kyoto encyclopedia of genes and genomes (KEGG) analysis. (frontiersin.org)
Comparison of gene expression levels between pools and treatments identified candidate genes for further analysis of the genetic basis of drought tolerance in red clover. (biomedcentral.com)
We sequenced the transcriptome of infected TGs from tree shrews and mice, and 4 human donors, then examined viral genes expression up to 58 days in infected TGs from mouse and tree shrew, and compare the latency data with that in human TGs. (biomedcentral.com)
We identified the dynamic transcriptome and enriched pathways of differentially expressed genes between day-8 and day-1 through DVID enrichment analysis and Gene Set Enrichment Analysis. (biomedcentral.com)
Despite the above studies that focused on specific genes or categories of genes, there are few papers which provide characterization of the microglial transcriptome following alcohol treatment or consumption. (biomedcentral.com)

Dedicated buffers and reagents undergo a unique, controlled decontamination procedure to block amplification of contaminating nucleic acids by the REPLI-g method. (qiagen.com)
The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing. (genomeweb.com)

Antisense transcription in the mammalian transcriptome. (nih.gov)

This method is flexibly applicable to both targeted and genome-wide analyses of absolute expression levels of mRNAs. (elsevierpure.com)
Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer. (who.int)

Genome characterization and p-distance analyses based on complete open reading frames revealed that the virus is probably a natural reassortant of the Echarate virus (large and small segments) with a yet-unidentified phlebovirus (M segment). (cdc.gov)
It not only provides a transcriptome characterization of HeLa S3 cells at the single cell level, but is a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers. (rna-seqblog.com)
In a pilot study of cervical samples obtained from women at high risk for STIs, we examined the potential for unbiased characterization of host, pathogen and microbiome interactions using whole transcriptome sequencing analysis of ribosomal RNA-depleted total RNAs (Total RNA-Seq). (microbialcell.com)

To increase our understanding of these differentially expressed unigenes, we performed Gene ontology and KEGG pathway enrichment analyses. (biomedcentral.com)
Intersecting analysis, molecular docking, and pathway validation analysis showed that risperidone influences the adipocytokine signaling pathway by targeting MAPK14 (mitogen-activated protein kinase 14), MAPK8 (mitogen-activated protein kinase 8), and RXRA (retinoic acid receptor RXR-alpha), thereby inhibiting long-chain fatty acid β-oxidation by decreasing STAT3 (signal transducer and activator of transcription 3) expression and phosphorylation. (frontiersin.org)
While pathway analysis identified many microglial associated functions, only a single study has directly examined the transcriptome of microglia acutely isolated from cortex of alcohol-fed mice [ 24 ]. (biomedcentral.com)

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. (nature.com)
RNA Sanger sequencing analysis was performed in AEG‑1‑deficient HT22 cells and wild‑type HT22 cells without knockout (KO). (spandidos-publications.com)
Orthologues identified by transcriptome sequencing were characterized using phylogenetic, ab initio protein modelling and comparative and population-based methods. (biomedcentral.com)
RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer. (nih.gov)
Second, a global view of the transcriptome of C. cassiicola spores during germination was evaluated using RNA sequencing (RNA-Seq). (biomedcentral.com)
Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins. (nanoporetech.com)
These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes. (biomedcentral.com)
We employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. (biomedcentral.com)
This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry. (biomedcentral.com)
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. (genomeweb.com)
A comparison of next-generation sequencing and clone-based sequencing in analysis of HBV RT quasispecies heterogeneity. (genomeweb.com)
We have also obtained transcriptome sequencing from total RNA submitted for gene expression analysis (NovoGene) of control and degenerating DLMs. (emerging-researchers.org)
Transcriptome sequencing revealed the presence of transcripts for Apolipophorin III identical to the published house cricket sequence and highly homologous for another cricket, Gryllus Bimaculatus. (emerging-researchers.org)
I helped review results for the transcriptome sequencing using NCBI blast and clustal alignment tools. (emerging-researchers.org)
Agnostic metagenomic analysis of clinical samples based on next-generation sequencing (NGS) combined with specifically designed PCRs constitute promising tools for diagnosing infection with unforeseen or novel microorganisms ( 8 ). (cdc.gov)
The authors would like to acknowledge Clinical Genomics Lund, SciLifeLab and Center for Translational Genomics (CTG), Lund University, for providing expertise and service with sequencing and analysis. (lu.se)

QIAseq UPX 3' Transcriptome Kits enable high-throughput gene expression analysis from cell lysates and isolated total RNA. (qiagen.com)
We applied a range of molecular and cellular techniques to measure cell survival, cell cycle progression, protein expression and DNA damage combined with a transcriptomic micro-array approach in D283-MED cells, for global gene expression analysis in acute and chronic hypoxic conditions. (biomedcentral.com)

Functional analysis of cfRNA suggests that is more promising than amniocyte RNA as a source of potential biomarkers of fetal neurodevelopment [ 3 ]. (biomedcentral.com)
LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification. (lu.se)

In that study, over 400 transcripts were identified in the microglial that were not present in pre-frontal cortical RNA [ 22 ], suggesting that cell type enrichment is necessary to fully characterize the effects of alcohol on the microglial transcriptome. (biomedcentral.com)

Library complexity is assessed using qPCR prior to amplification. (utmb.edu)
RNAseq analysis of microglia exposed for 24 h to alcohol identified 312 differentially expressed mRNAs ("Alc-DEs"), with changes confirmed by qPCR analysis. (biomedcentral.com)
Further analysis will include qPCR with samples collected from a more complete experimental design to allow for direct comparison of muscles and JH status. (emerging-researchers.org)

It is a multidisciplinary field that involves molecular analysis, biodefence, molecular biology, and microelectronics. (wikipedia.org)
QIAseq UPX 3' Transcriptome Kits are intended for molecular biology applications. (qiagen.com)

The assay is optimized to work with our BD Rhapsody™ Single-Cell Analysis System workflow, which enables higher capture rates than currently available solutions, preserving fragile cells in the process. (bdbiosciences.com)

One of the most striking results from the expression analysis was that the drought sensitive plants were characterised by having approximately twice the number of differentially expressed transcript tags than the tolerant plants after drought. (biomedcentral.com)

However, a recent pooled analysis of more than 3500 patients across four trials, published in The Lancet Oncology in 2021, revealed that patients with HER2 low tumors had fewer grade 3 tumors, lower tumor proliferation, and improved disease-free survival (DFS), in particular, patients with hormone receptor negative (HR) disease. (medscape.com)

Gene ontology analysis identified phagosome as one of the highest-ranking KEGG pathways including transcripts regulating phagocytosis. (biomedcentral.com)

Only samples from women with STI infection contained pathogen-specific sequences (3 to 38% transcriptome coverage). (microbialcell.com)

The isolated RNA is of sufficiently high quality, giving reproducible qRT-PCR results, for transcriptome analysis after RNA amplification. (altmetric.com)

BD has continued to build on its BD Rhapsody™ Single-Cell Analysis System, a comprehensive portfolio of reagents, instruments, software and targeted gene panels, to offer additional single-cell analysis capabilities. (bdbiosciences.com)
The REPLI-g Cell WGA & WTA Kit contains the novel REPLI-g SensiPhi DNA Polymerase, as well as an optimized set of buffers and reagents for parallel whole genome amplification (WGA) and whole transcriptome amplification (WTA) from 25-1000 cells, or equivalently small samples. (qiagen.com)

Using the well-annotated Saccharomyces cerevisiae transcriptome as a benchmark, we compared seven library-construction protocols, including both published and our own methods. (nature.com)
There was considerable discussion of adding value to the transcriptome by way of annotation methods, yet none of the annotations can be tied to actual sequence data. (peerj.com)
To date, our methods of antenatal prediction of long term neurodevelopmental outcome has been confined to only a few modalities-imaging with ultrasound and MRI, and maternal blood analysis for markers of aneuploidy or neural tube defects. (biomedcentral.com)

Zika virus infection modulates the bacterial diversity associated with Aedes aegypti as revealed by metagenomic analysis. (cdc.gov)

2015) Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells . (rna-seqblog.com)

Our data provided a landscape of the transcriptome and DNA methylome and revealed a candidate network that regulates flowering time in pineapple, which may promote further studies. (nature.com)
Analyze 3' RNA-seq data with ease using the GeneGlobe-integrated RNA-seq Analysis Portal - an intuitive, web-based data analysis solution created for biologists and included with QIAseq UPX 3' Transcriptome Kits. (qiagen.com)
Rachael Workman from Johns Hopkins presented transcriptome data generated through the Most Interesting Genome SMRT Grant program for the ruby-throated hummingbird, Archilochus colubris . (pacb.com)
On day-1 and day-8, clinical and laboratory data, as well as blood samples, were collected for RNA-Seq analysis. (biomedcentral.com)
View the poster for further data analysis information. (nanoporetech.com)
Nanopore read depth is more uniform than the bisulfite data (Fig. 1b), maps completely to the genome (Fig. 1c) and requires far less analysis time than bisulfite data (Fig. 1d). (nanoporetech.com)
Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution. (genomeweb.com)
It would help not only to precisely grasp the structure of the transcriptome but also to accelerate data exchange and integration. (elsevierpure.com)
Since the former contains every gene exactly at the same copy number, it can serve as an ideal normalization standard for the latter to obtain stoichiometric composition data of the transcriptome. (elsevierpure.com)

In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. (biomedcentral.com)

In contrast to PCR-based amplification technologies, high fidelity rates are increased up to 1000-fold, avoiding costly false positive or negative results. (qiagen.com)
However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. (biomedcentral.com)

Outbreak of Zika virus infection in Singapore: an epidemiological, entomological, virological, and clinical analysis. (cdc.gov)
Clinical and genetic analyses of a Swedish patient series diagnosed with ataxia. (lu.se)

STAMPs are then used as templates for PCR amplification, resulting in an expression library, each sequence of which is tagged with a barcode mapping it back to the cell of origin. (chemyx.com)
We utilized real time quantitative reverse transcriptase polymerase chain reaction (qRT PCR) in conjunction with agarose gel electrophoresis to establish protocols for analysis of the expression of transcripts of apolipophorin in the ovary, DLMs, fat body and femoral leg muscle of crickets undergoing the normal course of histolysis and from crickets ligated to prevent circulation of JH. (emerging-researchers.org)

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. (nature.com)

. pilosum and compared the transcriptomes of plants grown under normal and low temperatures. (biomedcentral.com)

Alternative isoform regulation in human tissue transcriptomes. (nature.com)

Key metabolites were measured and RNA-Seq analysis was carried out on four bulked samples: the two pools sampled before and after drought. (biomedcentral.com)

To identify the role that fibroblasts play during this process we have optimised a fibroblast isolation procedure, followed by cell cleanup, RNA extraction, and amplification from non-cultured, freshly isolated fibroblasts from around the TEB as well as the subtending ducts. (altmetric.com)

To further knowledge of the immune system, BD empowers immunology researchers with a range of tools for multiomic analysis. (bdbiosciences.com)

Analysis of the transcriptome identified several orthologues required for intra-erythrocytic survival and erythrocyte invasion, including the rhoptry neck protein 2 (RON2) and the apical membrane antigen-1 (AMA-1). (biomedcentral.com)

A detailed transcriptomic analysis of the tree shrew model could provide mechanistic insights into HSV-1 infection in humans. (biomedcentral.com)

The amplification product was submitted for DNA sequence analysis and the sequence was compared (98% identity) to published gene records using the NIH MegaBlast analysis tools. (emerging-researchers.org)

This is the first study to assess the cold-responsive transcriptome in an Ocimum species. (biomedcentral.com)
While the full analysis is still underway, Workman shared some interesting examples, such as the complete coverage of a glucose transporter gene that shows quite a bit of divergence across avian species. (pacb.com)

We offer tools for genomics analysis, protein analysis, and antibody screening techniques to provide a comprehensive approach to antigen discovery. (sigmaaldrich.com)

Single-cell analysis tools like the BD Rhapsody™ TCR/BCR Multiomic Assay and BD Rhapsody™ Single-Cell Analysis System support our customers need for greater sensitivity and specificity studying cells of interest and drive rapid advancements in immunology, including research in therapeutic response and cell therapy. (bdbiosciences.com)
In addition, BD also offers customers the option to conjugate their in-house antibodies of interest with oligos compatible with the BD Rhapsody™ Single-Cell Analysis System to generate custom BD® AbSeq Antibodies. (bdbiosciences.com)

Global Transcriptome Analysis of Aedes aegypti Mosquitoes in Response to Zika Virus Infection. (cdc.gov)
Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification. (cdc.gov)

An analysis of cotton showed that a short-read assembly was missing nearly 500 Mb of sequence, which was recovered in the PacBio assembly. (pacb.com)
The present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. (biomedcentral.com)

The LE and HE treatments induced drastic changes in transcriptome and DNA methylome, with LE inducing the initial response to flower induction and HE inducing the subsequent response. (nature.com)

Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in other organisms. (nature.com)
Therefore, a well-assembled, accurate, and comprehensive transcriptome is a prerequisite for the subsequent analysis. (biomedcentral.com)

After network pharmacology and GO analysis, risperidone was found to influence cellular metabolism. (frontiersin.org)
In addition, risperidone influences adipocyte metabolism, differentiation, and lipid accumulation-related functions through transcriptome analysis. (frontiersin.org)

Transcripts were identified from non-degenerating as well as degenerating DLMs in our PCR studies and in our transcritptome analysis. (emerging-researchers.org)

Diseases6

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