BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

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Identification of HMX1 target genes: A predictive promoter model approach

Purpose: A homozygous mutation in the H6 family homeobox 1 (HMX1) gene is responsible for a new oculoauricular defect leading to eye and auricular developmental abnormalities as well as early retinal degeneration (MIM 612109). However, the HMX1 pathway rem ...

Molecular Vision2013

PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Christof Holliger, Julien Maillard, Pierre Rossi, David Gregory Weissbrodt, Jacques Rougemont, Noam Shani, Lucas Sinclair

Background: In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microb ...

BioMed Central2012

Histone methyl transferases and demethylases; can they link metabolism and transcription?

Johan Auwerx, Kristina Schoonjans

Heritable changes to the transcriptome that are independent to changes in the genome are defined as epigenetics. DNA methylation and posttranslational modifications of histones, such as acetylation/deacetylation and methylation/demethylation of lysine resi ...

Cell Press2010

Gene expression profiling in cells with enhanced gamma-secretase activity

Patrick Fraering, Alexandra Marie-Isabelle Karoline Brigitte Magold

BACKGROUND: Processing by gamma-secretase of many type-I membrane protein substrates triggers signaling cascades by releasing intracellular domains (ICDs) that, following nuclear translocation, modulate the transcription of different genes regulating a div ...

Public Library of Science2009

Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR

Stewart Cole, Iain Old

BACKGROUND: Phi29 polymerase based amplification methods provides amplified DNA with minimal changes in sequence and relative abundance for many biomedical applications. RNA virus detection using microarrays, however, can present a challenge because phi29 ...

2008

Gene Expression Measurements by Quantitative Real-time PCR Depends on Short Amplicons and a Proper Normalization

Darlene Goldstein

Quantitative reverse transcriptase real-time PCR (QRT-PCR) is a robust method to quantitate RNA abundance. The procedure is highly sensitive and reproducible as long as the initial RNA is intact. However, breaks in the RNA due to chemical or enzymatic clea ...

2005

Statistical and experimental analysis of quantitative PCR

Quantitative PCR (qPCR) is a powerful technique that is now commonly used in many research and clinical laboratories. Although it allows precise quantification of specific DNA sequences, it is often not used at its full potential. A number of data collecti ...

EPFL2005

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PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Christof Holliger, Julien Maillard, Pierre Rossi, David Gregory Weissbrodt, Jacques Rougemont, Noam Shani, Lucas Sinclair

BioMed Central2012