RNA sequencing
Unprecedented High Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing
... RNA sequencing. RNA was prepared by using an RNeasy kit (Qiagen, ...stationary-phase RNA were treated with Terminator 5=-phosphate-dependent exonuclease (Epicenter, USA) to enrich 5=- ...
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Splatter: simulation of single cell RNA sequencing data
... In “Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data” [19] Lun and Marioni extended the negative binomial model from the Lun simulation. This simulation samples ...
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Aberrant modulation of the BRCA1 and G1/S cell cycle pathways in alcoholic hepatitis patients with Mallory Denk Bodies revealed by RNA sequencing
... by RNA sequencing (RNA-Seq), there was significant upregulation of BRCA1-mediated signaling and G1/S cell cycle checkpoint ...the RNA-Seq data that represents the fully annotated catalogue of ...
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The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development
... by RNA sequencing (RNA-Seq) revealed astonishing differences in gene expression between E12 −/− and E47 −/− primary embryonic NSCs when compared with their respective littermate wild-type controls ...
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ISEV position paper: extracellular vesicle RNA analysis and bioinformatics
... the sequencing platform employed; the adapter sequences vary widely and may introduce bias, which needs to be assessed (see paragraph on library ...for RNA detection is employed to preferably validate the ...
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RNA processing in the minimal organism Nanoarchaeum equitans
... small RNA molecules in N. equitans. Depending on the chosen method of RNA isolation, library preparation and employed RNA sequencing platform, different RNA spe- cies are selectively ...
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Original Article Chronic stress reduces spermatogenic cell proliferation in rat testis
... an RNA sequencing (RNA-seq) approach, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and immunohisto- chemistry, we investigated the changes in tes- ticular spermatogenic cell ...
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A genomic data viewer for iPad
... Tracks > Public Tracks menu lists a number of sample public datasets that are relevant for the currently se- lected reference genome. These include DNA sequen- cing data from the 1000 Genomes project [3], RNA ...
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Use of RNA sequencing to evaluate rheumatic disease patients
... expression. RNA-seq was used to perform a comprehensive transcriptome analysis of primary human monocytes from eight healthy controls and nine SLE pa- tients, with no evidence of other ...
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Biomarkers from circulating neutrophil transcriptomes have potential to detect unruptured intracranial aneurysms
... RNA sequencing data were used to identify differen- tially expressed neutrophil transcripts between the 15 patients with IA and 15 controls in the training ...our sequencing experiments had an ...
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Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes
... major RNA sequencing ...platforms. RNA-Seq of polyadenylated RNAs (A) or total RNA after rRNA depletion (B) enables profiling at a high resolution but requires a well-curated reference genome ...
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Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker
... and RNA was purified using the ALLPrep kit (Qiagen, ...to RNA sequencing whereas only 12 DNA samples were subjected to whole exome ...control RNA was collected from CD19+ blood B cells from ...
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RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA
... of RNA, providing cells with an- other mechanism to adjust transcript and protein levels in response to environmen- tal ...of RNA sequencing coverage of Escherichia coli and a corresponding RNase III ...
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LiBiNorm : an htseq count analogue with improved normalisation of Smart seq2 data and library preparation diagnostics
... preparing RNA sequencing (RNA-seq) libraries, most prominently “Smart-seq” variations, introduce global biases that can have a significant impact on the quantification of gene expression ...of ...
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Bmp signaling maintains a mesoderm progenitor cell state in the mouse tailbud
... Total RNA was obtained using the RNeasy Micro Kit (Qiagen) following the manufacturer’s ...above. Sequencing libraries were prepared by Genome Quebec Innovation Centre (Montreal, Canada) using the TruSeq ...
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Ultrasensitive single genome sequencing: accurate, targeted, next generation sequencing of HIV 1 RNA
... To help address these issues, primer IDs, consisting of molecular tags comprising 4–10 degenerate nucleotides (nt), have been incorporated into RT primers so that each cDNA molecule generated by reverse transcription is ...
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An RNA editing fingerprint of cancer stem cell reprogramming
... each RNA editing site, two sets of primers were designed: one pair detecting the WT transcript (an “A” base), and one pair detecting the edited transcript containing a “G” base representing inosine substitution ...
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Transcriptomic approaches to understanding ageing and metabolism in rodents
... using Bowtie (Langmead et al., 2009) and settings appropriate to SOLiD data. For each sample, approximately 33.6 million reads were generated (range, 29.5 to 39.8 million reads). On average 16.7 million reads per sample ...
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Scalable microfluidics for single cell RNA printing and sequencing
... Illumina sequencing adapter (ISA) comprise the 5′-end of the capture primer (Additional file 1: Table S1) to allow linear pre-amplification by in vitro transcription (IVT) and library enrichment by PCR ...
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IVT seq reveals extreme bias in RNA sequencing
... SP6 RNA polymerase, and 10 μl of RNase-free ...of RNA was assessed by agarose gel electro- ...IVT RNA to confirm total depletion of plasmid ...
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