Search · four archives

Results for transcriptome quantification

or ask it as a questionAsk the stacks →

ArchivesarXiv PubMed bioRxiv chemRxiv

WhenAny time Past month Past year Past 5 years

OrderMost relevant Most cited Newest

15 papers · ranked by Valyu relevance

01
BbioRxiv31 Jul 2018
Effect of *de novo* transcriptome assembly on transcript quantification
Ping-Han Hsieh, Yen-Jen Oyang, Chien-Yu Chen
Correct quantification of transcript expression is essential to understand the functional products of the genome in different physiological conditions and developmental stages. Recently, the development of high-throughput RNA sequencing (RNA-Seq) allows the researchers to perform transcriptome analysis for the…
83relevance
02
BbioRxiv29 Nov 2018
CoCo: RNA-seq Read Assignment Correction for Nested Genes and Multimapped Reads
Gabrielle Deschamps-Francoeur, Vincent Boivin, Sherif Abou Elela, Michelle S Scott
Next generation sequencing techniques revolutionized the study of RNA expression by permitting whole transcriptome analysis. However, sequencing reads generated from nested and multi-copy genes are often either misassigned or discarded, which greatly reduces both quantification accuracy and gene coverage. Here we…
80relevance
03
BbioRxiv6 May 2016
AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in *Arabidopsis thaliana* RNA-seq data
Runxuan Zhang, Cristiane P. G. Calixto, Yamile Marquez, Peter Venhuizen + 10 more
Alternative splicing is the major post-transcriptional mechanism by which gene expression is regulated and affects a wide range of processes and responses in most eukaryotic organisms. RNA-sequencing (RNA-seq) can generate genome-wide quantification of individual transcript isoforms to identify changes in expression…
80relevance
04
BbioRxiv29 Mar 2024
Real-time transcriptomic profiling in distinct experimental conditions
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer + 6 more
Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis…
78relevance
05
BbioRxiv12 Aug 2016
Highly parallel direct RNA sequencing on an array of nanopores
Daniel R. Garalde, Elizabeth A. Snell, Daniel Jachimowicz, Andrew J. Heron + 19 more
Ribonucleic acid sequencing can allow us to monitor the RNAs present in a sample. This enables us to detect the presence and nucleotide sequence of viruses, or to build a picture of how active transcriptional processes are changing – information that is useful for understanding the status and function of a sample.…
78relevance
06
BbioRxiv14 May 2014
RNA-seq gene profiling - a systematic empirical comparison
Nuno A. Fonseca, John Marioni, Alviz Brazma
Accurately quantifying gene expression levels is a key goal of experiments using RNA-sequencing to assay the transcriptome. This typically requires aligning the short reads generated to the genome or transcriptome before quantifying expression of pre-defined sets of genes. Differences in the alignment/quantification…
77relevance
07
BbioRxiv28 Apr 2021
Transcriptome diversity is a systematic source of bias in RNA-sequencing data
Pablo E. García-Nieto, Ban Wang, Hunter B. Fraser
RNA sequencing has been widely used as an essential tool to probe gene expression. While standard practices have been established to analyze RNA-seq data, it is still challenging to detect and remove artifactual signals. Several factors such as sex, age, and sequencing technology have been found to bias these…
74relevance
08
BbioRxiv22 Aug 2015
Snake venom gland cDNA sequencing using the Oxford Nanopore MinION portable DNA sequencer
Adam D Hargreaves, John F Mulley
Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we…
74relevance
09
BbioRxiv30 Apr 2015
Controlling False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data
David M. Rocke, Luyao Ruan, J. Jared Gossett, Blythe Durbin-Johnson + 1 more
We review existing methods for the analysis of RNA-Seq data and place them in a common framework of a sequence of tasks that are usually part of the process. We show that many existing methods produce large numbers of false positives in cases where the null hypothesis is true by construction and where actual data from…
73relevance
10
BbioRxiv28 Dec 2015
The impact of amplification on differential expression analyses by RNA-seq
Swati Parekh, Christoph Ziegenhain, Beate Vieth, Wolfgang Enard + 1 more
Currently quantitative RNA-Seq methods are pushed to work with increasingly small starting amounts of RNA that require PCR amplification to generate libraries. However, it is unclear how much noise or bias amplification introduces and how this effects precision and accuracy of RNA quantification. To assess the effects…
72relevance
11
BbioRxiv1 Feb 2025
Simultaneous profiling of native-state proteomes and transcriptomes of neural cell types using proximity labeling
Christina C. Ramelow, Eric B. Dammer, Hailian Xiao, Lihong Cheng + 13 more
Deep molecular phenotyping of cells at transcriptomic and proteomic levels is an essential first step to understanding cellular contributions to development, aging, injury, and disease. Since proteome and transcriptome level abundances only modestly correlate with each other, complementary profiling of both is needed.…
72relevance
12
BbioRxiv15 Nov 2019
RNA Sequencing by Direct Tagmentation of RNA/DNA Hybrids
Lin Di, Yusi Fu, Yue Sun, Jie Li + 13 more
Transcriptome profiling by RNA sequencing (RNA-seq) has been widely used to characterize cellular status but it relies on second strand cDNA synthesis to generate initial material for library preparation. Here we use bacterial transposase Tn5, which has been increasingly used in various high-throughput DNA analyses, to…
71relevance
13
BbioRxiv31 Jan 2017
A Multi-Parameter Analysis of Cellular Coordination of Multiple Transcriptome Regulation Mechanisms
Wen Jiang, Zhanyong Guo, Nuno Lages, W. Jim Zheng + 3 more
To understand cellular coordination of multiple transcriptome regulation mechanisms, we simultaneously measured three parameters – transcription rate (TR), mRNA abundance (RA) and translation activity (TA) – and assessed mRNA stability with the RA to TR ratio. This revealed multiple quantitative insights. First, the…
71relevance
14
BbioRxiv10 Nov 2014
Comprehensive comparison of large-scale tissue expression datasets
Alberto Santos, Kalliopi Tsafou, Christian Stolte, Sune Pletscher-Frankild + 2 more
For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated. We present a comprehensive evaluation…
68relevance
15
BbioRxiv10 Jun 2014
Validation of methods for Low-volume RNA-seq
Peter A. Combs, Michael B. Eisen
Recently, a number of protocols extending RNA-sequencing to the single-cell regime have been published. However, we were concerned that the additional steps to deal with such minute quantities of input sample would introduce serious biases that would make analysis of the data using existing approaches invalid. In this…
68relevance

Results for transcriptome quantification

Effect of de novo transcriptome assembly on transcript quantification

CoCo: RNA-seq Read Assignment Correction for Nested Genes and Multimapped Reads

AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data

Real-time transcriptomic profiling in distinct experimental conditions

Highly parallel direct RNA sequencing on an array of nanopores

RNA-seq gene profiling - a systematic empirical comparison

Transcriptome diversity is a systematic source of bias in RNA-sequencing data

Snake venom gland cDNA sequencing using the Oxford Nanopore MinION portable DNA sequencer

Controlling False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data

The impact of amplification on differential expression analyses by RNA-seq

Simultaneous profiling of native-state proteomes and transcriptomes of neural cell types using proximity labeling

RNA Sequencing by Direct Tagmentation of RNA/DNA Hybrids

A Multi-Parameter Analysis of Cellular Coordination of Multiple Transcriptome Regulation Mechanisms

Comprehensive comparison of large-scale tissue expression datasets

Validation of methods for Low-volume RNA-seq

Effect of de novo transcriptome assembly on transcript quantification

CoCo: RNA-seq Read Assignment Correction for Nested Genes and Multimapped Reads

AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data

Real-time transcriptomic profiling in distinct experimental conditions

Highly parallel direct RNA sequencing on an array of nanopores

RNA-seq gene profiling - a systematic empirical comparison

Transcriptome diversity is a systematic source of bias in RNA-sequencing data

Snake venom gland cDNA sequencing using the Oxford Nanopore MinION portable DNA sequencer

Controlling False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data

The impact of amplification on differential expression analyses by RNA-seq

Simultaneous profiling of native-state proteomes and transcriptomes of neural cell types using proximity labeling

RNA Sequencing by Direct Tagmentation of RNA/DNA Hybrids

A Multi-Parameter Analysis of Cellular Coordination of Multiple Transcriptome Regulation Mechanisms

Comprehensive comparison of large-scale tissue expression datasets

Validation of methods for Low-volume RNA-seq

Results for transcriptome quantification

Effect of *de novo* transcriptome assembly on transcript quantification

CoCo: RNA-seq Read Assignment Correction for Nested Genes and Multimapped Reads

AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in *Arabidopsis thaliana* RNA-seq data

Real-time transcriptomic profiling in distinct experimental conditions

Highly parallel direct RNA sequencing on an array of nanopores

RNA-seq gene profiling - a systematic empirical comparison

Transcriptome diversity is a systematic source of bias in RNA-sequencing data

Snake venom gland cDNA sequencing using the Oxford Nanopore MinION portable DNA sequencer

Controlling False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data

The impact of amplification on differential expression analyses by RNA-seq

Simultaneous profiling of native-state proteomes and transcriptomes of neural cell types using proximity labeling

RNA Sequencing by Direct Tagmentation of RNA/DNA Hybrids

A Multi-Parameter Analysis of Cellular Coordination of Multiple Transcriptome Regulation Mechanisms

Comprehensive comparison of large-scale tissue expression datasets

Validation of methods for Low-volume RNA-seq

Effect of *de novo* transcriptome assembly on transcript quantification

CoCo: RNA-seq Read Assignment Correction for Nested Genes and Multimapped Reads

AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in *Arabidopsis thaliana* RNA-seq data

Real-time transcriptomic profiling in distinct experimental conditions

Highly parallel direct RNA sequencing on an array of nanopores

RNA-seq gene profiling - a systematic empirical comparison

Transcriptome diversity is a systematic source of bias in RNA-sequencing data

Snake venom gland cDNA sequencing using the Oxford Nanopore MinION portable DNA sequencer

Controlling False Positive Rates in Methods for Differential Gene Expression Analysis using RNA-Seq Data

The impact of amplification on differential expression analyses by RNA-seq

Simultaneous profiling of native-state proteomes and transcriptomes of neural cell types using proximity labeling

RNA Sequencing by Direct Tagmentation of RNA/DNA Hybrids

A Multi-Parameter Analysis of Cellular Coordination of Multiple Transcriptome Regulation Mechanisms

Comprehensive comparison of large-scale tissue expression datasets

Validation of methods for Low-volume RNA-seq

Effect of de novo transcriptome assembly on transcript quantification

AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data

Effect of de novo transcriptome assembly on transcript quantification

AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data