Transcriptome seq. Medical search. Frequent questions

In this study, differentially expressed genes (DEGs) under drought and flooding conditions were investigated using Illumina RNA-Seq transcriptome profiling. (frontiersin.org)

RNA (total, poly A+ and miRNA), chromatin immunoprecipitated DNA (ChIP-Seq) and DNA (genomic and amplicon-derived). (utmb.edu)
Very few ChIP-chip/seq of ABA-related TFs have been reported to date. (nih.gov)
To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. (nih.gov)
Analyses of the resulting 122 ChIP-seq datasets identified 326,698 TF binding events using a stringent statistical cutoff. (nih.gov)
In addition to RNA-seq, other NGS-based techniques such as various forms of DNA-analysis and ChIP-seq are available upon request. (lu.se)

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)
Detailed analysis of the splicing junctions showed clusters of AS events occurred in two regions of the virus genome, demonstrating that transcriptome analysis could gain valuable insights into viral splicing. (nature.com)
Transcriptome analysis is a powerful approach to research grain traits and elucidate their genetic regulation. (engineering.org.cn)
AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. (dundee.ac.uk)
It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. (dundee.ac.uk)
Transcriptome analysis is a powerful tool that enables a deep understanding of complicated physiological pathways, including immune responses. (frontiersin.org)
RNA sequencing (RNA-Seq)-based transcriptome analysis and various bioinformatics tools have also been used to study non-model animals, including aquaculture species for which reference genomes are not available. (frontiersin.org)
In the first one, the complete analysis for junction arrays is described and the second one describes the analysis for RNA-Seq data. (bioconductor.org)
Cell type-specific transcriptome analysis is an essential tool for understanding biological processes in which diverse types of cells are involved. (nih.gov)
Although cell isolation methods such as fluorescence-activated cell sorting (FACS) in combination with transcriptome analysis have widely been used so far, their time-consuming and harsh procedures limit their applications. (nih.gov)
Finally, we have performed RNA-seq analysis of neutrophils and lungs and found that while Ager −/− mice had a broad alteration of transcriptome in both tissues compared to wild-type mice, the changes of transcriptome in Ager AHA/AHA mice were much more restricted. (elifesciences.org)
The complete solution includes online access to the RNA-seq analysis portal (for supported species), which allows researchers to start with FASTQ files and perform read alignment, differential gene expression and pathway analysis. (qiagen.com)
To see demo data, log in to the RNA-seq Analysis Portal and go to the QIAseq FastSelect RNA Library folder. (qiagen.com)
Is the Subject Area "Transcriptome analysis" applicable to this article? (plos.org)
Analyze stranded 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 Stranded RNA Library Kits. (qiagen.com)
Cell Ranger is a set of analysis pipelines that processes Chromium single-cell 3′ RNA-Seq output to align reads, generate gene-cell matrices, and perform clustering and gene-expression analysis. (genengnews.com)
METHODS: We sorted a SCC into CD133- and CD133+ subpopulations and then examined both by copy number analysis (CNA) and whole genome and transcriptome sequencing. (ca.gov)
The Personalized OncoGenomics (POG) program at BC Cancer performs whole genome and transcriptome analysis (WGTA) to identify specific alterations in an individual's cancer tha. (researchgate.net)
In this study, we evaluate the impact of whole genome and transcriptome analysis (WGTA) on predictive molecular profiling and histologic diagnosis in a cohort of advanced malignancies. (researchgate.net)
For instance, you can create a pipeline that can preprocess reads, map them to a reference genome, count reads that are mapped to genomic features, and perform a statistical analysis, such as a differential expression analysis or genome-wide analysis from RNA-Seq or ChIP-Seq data. (mathworks.com)
The core offers state-of-the art next generation sequencing technology for experimental and preclinical studies with particular expertise in transcriptome analysis. (lu.se)

Single-cell RNA-Seq allows heterogeneities within a population to be captured," Dr. Hindson stated. (genengnews.com)

Here, we integrated isoform sequencing (iso-seq), Illumina short-reads sequencing and whole-genome bisulfite sequencing (WGBS) to explore the early changes of transcriptomic and DNA methylation in pineapple following high-concentration ethylene (HE) and low-concentration ethylene (LE) treatment. (nature.com)
The Ambion® RNA-Seq Library Construction Kit streamlines high-throughput sequencing of the whole transcriptome and small RNAs, while maintaining strand orientation, on the Illumina® GAII platform. (thermofisher.com)
Do you currently perform RNA-Seq on the Illumina® platform, or plan to within the next two months? (thermofisher.com)
QIAseq Stranded RNA Library Kits provide a superior method for generating Illumina compatible RNA-seq libraries from total RNA or mRNA enriched samples. (qiagen.com)

QIAseq FastSelect RNA Library Kits are versatile and contain all the reagents to make stranded RNA-seq libraries for complete transcriptomics or 3' RNA-seq, depending on the workflow selected and type of RNA used. (qiagen.com)

Results: We performed comparative RNA-Seq transcriptomic analyses to assess the carcinogenic effects of 600 MeV/n 56Fe (0.2 Gy), 1 GeV/n 16O (0.2 Gy), and 350 MeV/n 28Si (0.2 Gy) ions in a mouse model for irradiation-induced HCC. (utmb.edu)

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)
Our de novo assembly of RNA-Seq data produced a large set of sequences which included many duplicates and fragments. (biomedcentral.com)

As increasing number of next-generation sequencing (NGS) datasets are being produced from various-omics initiatives, transcriptome sequencing of flora and fauna for a specific developmental stage/condition gains its popularity in biological research. (nature.com)

Researchers can also utilize mRNA enrichment kits (sold separately) and focus RNA-seq library construction on protein coding mRNAs. (qiagen.com)
RNA-seq libraries have been successfully constructed from high-quality total RNA, fragmented FFPE RNA and enriched mRNA. (qiagen.com)
To assess genomic changes, we quantified mRNA expression using high throughput sequencing technologies (RNA-Seq) in F. grandis populations in the marshes and estuaries impacted by DH oil release. (biomedcentral.com)
For applications such as gene expression, fusion gene or mutation detection, QIAseq Stranded mRNA Select Kits include an optimized mRNA enrichment protocol with all the reagents and components required to build high-quality RNA-seq libraries. (qiagen.com)

For arrays, the SG is built according to the reference transcriptome selected by the user and for RNA-Seq, it is created by predicting the features in the .bam files provided by the user. (bioconductor.org)
To build the CDF file (to work under the aroma.affymetrix framework), EventPointer requires a GTF file with the reference transcriptome information. (bioconductor.org)
In this study we assembled a reference transcriptome from representative natural populations of F. grandis collected from Gulf Coast estuaries ranging from Texas to Florida. (biomedcentral.com)

AtRTD3 contains over 169,000 transcripts-twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. (dundee.ac.uk)
Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. (dundee.ac.uk)
Researchers used PacBio's Iso-Seq method to sequence full-length cDNA transcripts from ripening Cabernet Savignon berries resulting in 1,5000 cultivar-specific genes. (sagescience.com)
In the aquaculture field, there is wide utility for RNA-Seq in various applications, such as understanding the development of embryo and larvae, toxicology, environmental stress, effect of dietary conditions, and discovery of novel transcripts ( 2 - 4 ). (frontiersin.org)
To investigate the biological functions of these novel transcripts, we used a machine learning technique known as self-organizing maps (SOMs) to characterize the transcriptome expression profiles of 60 samples (45 HZE-irradiated, 15 non-irradiated control) from liver tissues. (utmb.edu)
Sequential assembly of the human spliceosome on RNA transcripts regulates splicing across the human transcriptome. (biomedcentral.com)
The final RNA-seq libraries created using the QIAseq FastSelect RNA Library Kits retain strand and directionality of the original transcript, increasing the accuracy of the final mapped transcripts and quantification. (qiagen.com)
For the purposes of RNA-Seq experiments, transcripts with highly redundant sequence should be removed. (stanford.edu)

rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome. (ox.ac.uk)
Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer. (ca.gov)
m 6 Am-seq reveals the dynamic m 6 Am methylation in the human transcriptome. (bvsalud.org)

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. (wikipedia.org)
Small RNA-Seq can analyze thousands of small RNA molecules with a high throughput and specificity. (wikipedia.org)

PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)

Transcriptome comparisons of SOX9+ cells with GLT1+ cells showed that the two populations of cells exhibit largely overlapping gene expression. (jneurosci.org)
The Human Cell Atlas relies, to a great extent, on the use of transcriptome sequencing to profile the gene expression of individual cells. (genengnews.com)
These results add another dimension to the use of RNA‐seq as a clinical tool, where both gene expression‐ and mutation‐based biomarkers can be interrogated in real‐time within 1 week of tumor sampling. (lu.se)
High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)

RNA sequencing (RNA-Seq) is a modern technology for transcriptome profiling that uses next-generation sequencing (NGS). (frontiersin.org)
We introduce RNA G-quadruplex sequencing (rG4-seq), a transcriptome-wide RNA G-quadruplex (rG4) profiling method that couples rG4-mediated reverse transcriptase stalling with next-generation sequencing. (ox.ac.uk)

Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm. (bioconductor.org)

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)
The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). (bioconductor.org)
Using the GemCode approach, Dr. Hindson and colleagues collected transcriptome data from about 250,000 cells across 29 samples. (genengnews.com)
We analyzed The Cancer Genome Atlas (TCGA) transcriptome data of 221 SCCs to determine the generality of our observations. (ca.gov)
SCC RNA-seq data (n = 221) from TCGA supported our findings. (ca.gov)
We reviewed whole genome (WGS) and transcriptomic (RNA-Seq) data from advanced GI and thoracic cancers in the Personalized OncoGenomics trial (NCT02155621) to evaluate HRD sc. (researchgate.net)
Our data demonstrate complex changes in the pneumococcal transcriptome in response to IAV-induced changes in the environment. (lu.se)

Here we report a novel approach to characterizing viral AS using whole transcriptome dataset from host species. (nature.com)

Here, we analyze the transcriptome of CSC and non-CSC subpopulations by RNA-seq to identify new potential therapeutic strategies for SCC. (ca.gov)

Advancements in bioinformatics has significantly supported RNA-Seq technology to accelerate the knowledge on transcriptomes ( 1 ). (frontiersin.org)

In this frame, one of the key aims of high throughput transcriptome sequencing is the detection of all RNA species present in the cell and the first crucial step for RNA-seq users is represented by the choice of the strategy for cDNA library construction. (uniba.it)
The BluePippn was used to size select 1-2 kbp, 2-3 kbp, 3-6 kbp, and 5-10 kbp fractions for cDNA SMRTbell library construction for the Iso-Seq method. (sagescience.com)
Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)

Within SCAN‐B (ClinicalTrials.gov: NCT02306096), a prospective study elucidating the transcriptomic profiles for thousands of breast cancers, we developed a RNA‐seq pipeline for detection of SNVs/indels and profiled a real‐world cohort of 3,217 breast tumors. (lu.se)

The lack of efficient and quantitative tRNA-seq methods has hindered biological studies of tRNA. (cdc.gov)

Here, we show that alterations in RNA splicing patterns across the human transcriptome that occur in conditions of restricted cellular PRPF8 abundance are defined by the altered splicing of introns with weak 5′ splice sites. (biomedcentral.com)

Next, 70 million raw reads were generated by RNA-seq of which 50% could be aligned with the horse reference genome. (uaeu.ac.ae)
We assembled the transcriptome of a clonal population of adult, aposymbiotic (dinoflagellate-free) Aiptasia pallida from ~208 million reads, yielding 58,018 contigs. (stanford.edu)

In Chenopodiaceae, a family that is rich in C 4 origins and photosynthetic types, the anatomy, physiology and phylogeny of C 4 , C 2 , and C 3 species of Salsoleae has been studied in great detail, which facilitated the choice of six samples of five representative species with different photosynthetic types for transcriptome comparisons. (nih.gov)
Herein we provide methodological detail and results of transcriptome expression comparisons between populations of F. grandis sampled directly from the environment affected by the DH oil release versus those from unaffected populations. (biomedcentral.com)

A platform independent RNA-Seq protocol for the detection of transcriptome complexity. (uniba.it)

We describe the mutational landscape of primary breast cancer viewed through the transcriptome of a large population‐based cohort and relate it to patient survival. (lu.se)

This method has successfully identified the cell type-specific transcriptome in three different tissues: endothelial cells in brain, epithelial cells in intestine and adipocytes in white adipose tissue. (nih.gov)
He added that this kind of sample preparation-which may involve samples supplied by different laboratories and taken from different tissues-is a challenge when RNA-Seq experiments are to be performed. (genengnews.com)

II intron reverse transcriptase to overcome these obstacles (DM-TGIRT-seq). (cdc.gov)

RNA-Seq may be successfully applied to feral and extremely polymorphic organisms that do not have an underlying genome sequence assembly to address timely environmental problems. (biomedcentral.com)
These contigs were uploaded to the NCBI Transcriptome Assembly Shotgun Sequence Database, accession numbers JV077153-JV134524. (stanford.edu)

In so doing, it demonstrates how transcriptome sequencing provides insights into the molecular underpinnings of cancer propagating cells that, importantly, can be leveraged to identify new potential therapeutic options for cancers beyond what is possible with DNA sequencing. (ca.gov)

Here we report the first characterization of the global transcriptome of the sperm of fertile stallions. (uaeu.ac.ae)

Approximate costs for one single RNA-seq sample typicalle range from 1000 SEK - 3000 SEK per sample but are dependent on the design of the project. (lu.se)

Experimental design: Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence. (researchgate.net)

Two insect transcriptomes ( Acheta domesticus and Planococcus citri ) generated in the 1,000 Insect Transcriptome Evolution (1KITE) project were used as a proof of concept using the new pipeline. (nature.com)

AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. (dundee.ac.uk)

Generating high-quality human reference genomes using PromethION nanopore seq. (slideshare.net)

2006). Reporter gene assays founded that the modification in manifestation of genes and grain (((iron insufficiency transcriptome in both presence and lack of acetate in the development medium. (irjs.info)

Anatomy22

Organisms37

Diseases2

Chemicals and Drugs37

Analytical, Diagnostic and Therapeutic Techniques and Equipment26

Phenomena and Processes90

Disciplines and Occupations5

Technology, Industry, Agriculture6

Information Science10

Health Care3

Expressed genes1

ChIP-Seq5

Analysis21

Single-cell RNA-Seq1

Illumina4

Stranded RNA-seq libraries1

Analyses1

Novo2

Datasets1

MRNA4

Reference transcriptome3

Transcripts8

Reveals3

Small RNA2

Genomic1

Gene expression4

Profiling2

Microarray1

Data7

Dataset1

Analyze1

Bioinformatics1

CDNA3

Transcriptomic1

Quantitative1

Splice1

Reads2

Comparisons2

Complexity1

Mutational landscape1

Tissues2

Reverse transcriptase1

Assembly2

Sequencing1

Characterization1

10001

Cancer1

Pipeline1

Arabidopsis1

Human1

Grain1