Deep sequencing
Deep Sequencing Analysis of the Ixodes ricinus Haemocytome.
... by deep sequencing a haemocyte cDNA library and by annotating immune-related transcripts based on their abundance in haemocytes and their sequence divergence when compared to their arthropod ...
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Identification and characterisation of microRNAs in young adults of Angiostrongylus cantonensis via a deep-sequencing approach
... a deep-sequencing approach, based on 7,548,965 reads, we identified and characterised 252 conserved mature miRNAs including 10 antisense miR- NAs that belonging to 90 families from young adults of ...
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Dynamics of hepatitis B virus quasispecies in association with nucleos(t)ide analogue treatment determined by ultra-deep sequencing.
... from sequencing errors in the determined sequences, we first generated viral sequence data from the expression plasmid, pcDNA3-HBV-wt#1, encoding wild-type genotype C HBV genome sequences ...as sequencing ...
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Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission.
... using deep sequencing in order to measure the amount of mutation occurring on a small time ...rabies, deep-sequencing was applied to 40 unpassaged rabies virus samples from the Humboldt ...
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RNA deep sequencing reveals novel candidate genes and polymorphisms in boar testis and liver tissues with divergent androstenone levels.
... For qRT-PCR experiment, total RNA from testis and liver samples were isolated from the 10 boars used for deep sequencing. Additionally, RNA was isolated from the similar tissues of 10 independent boars with ...
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Mutations Related to Antiretroviral Resistance Identified by Ultra-Deep Sequencing in HIV-1 Infected Children under Structured Interruptions of HAART.
... transcriptase inhibitors commercially available [6]. Despite the limitations of the number of patients analyzed, the results of that previous work suggested that STI, in the context evaluated, could be safe; however, ...
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Prevalence of WHO transmitted drug resistance mutations by deep sequencing in antiretroviral-naive subjects in Hunan Province, China.
... Using deep sequencing, we found that ART-naı¨ve subjects from Hunan Province, China, who were infected predominantly with subtype AE, frequently possessed HIV variants with WHO NRTI/NNRTI/PI TDRs that would ...
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Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq.
... cDNA sequencing approach not only detects association with Hfq, but also identifies the termini of expressed sRNAs at nucleotide-level ...cDNA sequencing and coIP-on-chip analyses of ESP-grown bacteria were ...
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Discovery of MicroRNAs associated with myogenesis by deep sequencing of serial developmental skeletal muscles in pigs.
... Developing pigs have a much longer embryonic period than mice; therefore, their development can be divided into more stages to obtain a more precise understanding of embryonic myogenesis. Many research groups have ...
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Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data.
... of deep sequencing data and thus converge towards the same set of ...high sequencing depth data only) return surprisingly high numbers of SNV calls in low agreement with other ...exome ...
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Profile of microRNAs following rat sciatic nerve injury by deep sequencing: implication for mechanisms of nerve regeneration.
... Unlike the central nervous system, peripheral nerves can regenerate when damaged. MicroRNA (miRNA) is a novel class of small, non-coding RNA that regulates gene expression at the post-transcriptional level. Here, we ...
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Deep sequencing-based transcriptome analysis of chicken spleen in response to avian pathogenic Escherichia coli (APEC) infection.
... (NC) but treated with 0.1 ml phosphate buffered saline (PBS). All detailed information on the APEC O1 strain and challenge design and procedures was previously described [22]. Birds were euthanized and necropsy was ...
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Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome.
... performed deep sequencing of the nuclear and organellar genomes of three mungbean genotypes: Vigna radiata ...performed deep sequencing of the RIL59 transcriptome to investigate transcript ...
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Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis.
... Deep sequencing after bisulfite conversion (BS-Seq) is the method of choice to generate whole genome maps of cytosine methylation at single base-pair ...(Bisufite Sequencing Scorer), a new method ...
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Metatranscriptomic analysis of small RNAs present in soybean deep sequencing libraries
... using deep-sequencing data, sig- nificant differences have been found in the taxonomic dis- tribution of cDNAs derived from total RNA compared to DNA libraries from soil samples (Bailly et ...sRNA ...
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Quantitative identification of mutant alleles derived from lung cancer in plasma cell-free DNA via anomaly detection using deep sequencing data.
... First, we examined the method’s quantification ability. We prepared test samples including various fractions of PCR products of mutated EGFR fragments. There was a very good linearity (r=0.998) between the inoculated ...
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Deep sequencing analysis reveals distinctive non-coding RNAs when comparing tumor multidrug-resistant cells and extracellular vesicles with drug-sensitive counterparts
... Abstract: Multidrug resistance (MDR) is one of the main limitations of cancer treatment. The overexpression of drug-efflux pumps, such as P-glycoprotein (P-gp), is a major cause of MDR. Importantly, different studies ...
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Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins.
... Somatic mutations of mtDNA are implicated in the aging process, but there is no universally accepted method for their accurate quantification. We have used ultra-deep sequencing to study genome-wide mtDNA ...
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Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer.
... temporal deep sequencing pattern defined by the ...A deep sequencing experiment, such as ChIP- seq, is followed by preprocessing in ...
13
RNA deep sequencing analysis reveals that nicotine restores impaired gene expression by viral proteins in the brains of HIV-1 transgenic rats.
... Persons infected with HIV-1 often develop neurologic disorders despite receiving highly active anti-retroviral therapy. Although the underlying mechanism is largely undetermined, our previous RNA-seq-based study showed ...
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