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Deep sequencing

Tìm thấy 20+ kết quả cho từ khóa "Deep sequencing"

The effect of variant interference on de novo assembly for viral deep sequencing

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Conclusions: These results call for careful interpretation of contigs and contig numbers from de novo assembly in viral deep sequencing.. Keywords: De novo assembly, Variant, Quasispecies, Virus, Microbe.

2C-ChIP: Measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

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List of primer sequences used to amplify 2C-ChIP libraries prior to deep sequencing on a PGM ™ system (Thermo Fisher Scientific). This folder contains the input-normalized 2C-ChIP data in BedGraph format of all the ChIP samples measured in this study.

High-throughput deep sequencing reveals the important role that microRNAs play in the salt response in sweet potato (Ipomoea batatas L.)

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High-throughput deep sequencing reveals the important role that microRNAs play in the salt response in sweet potato ( Ipomoea batatas L.). Sweet potato (Ipomoea batatas L.) is an important food and industrial crop that ranks seventh in staple food production. However, the regulatory mechanism of miRNA- mediated abiotic stress response in sweet potato remains unclear..

Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content

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Despite high coverage sequencing we were unable to detect sCNAs in plasma samples.. Conclusions: Deep sequencing analysis of plasma samples revealed higher fraction of unique somatic mutations in plasma samples, which were not detected in matched tumour samples. 7 Department of Infectious Disease, Imperial College London, London, UK Full list of author information is available at the end of the article.

Small RNA and degradome deep sequencing reveal respective roles of coldrelated microRNAs across Chinese wild grapevine and cultivated grapevine

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Here, sRNA and degradome deep sequencing were performed to detect and analyze cold-related miR- NAs and their target genes in Chinese wild grapevine.. For example, orthologous pairs include Chinese wild grape miR172a with culti- vated grape Vvi-172a. Chinese wild grape miR159a with cultivated grape Vvi-159a. and Chinese wild grape miR160b with cultivated grape Vvi-miR160b..

Identification and characterisation of microRNAs and their target genes in phosphate-starved Nicotiana benthamiana by small RNA deep sequencing and 5’RACE analysis

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Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation. A miRNA involved in phosphate- starvation response in Arabidopsis. A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae.

Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections

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Deep sequencing of short amplicons has the potential to overcome some of the shortfalls of length poly- morphic genotyping markers, in particular the influence of fragment length of a marker on the detectability of minority clones. vivax by amplicon deep sequencing: (i) Sequencing of the clas- sical length polymorphic genotyping markers, such as P..

Deep sequencing identification of miRNAs in pigeon ovaries illuminated with monochromatic light

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Herein, we harvested ovaries from pigeons reared under monochromatic light of different wavelength and performed deep sequencing on various tissues using an Illumina Solexa high-throughput instrument.. Three and five differentially expressed miRNAs were identified in BL vs. Quantitative reverse transcription PCR was used to validate differentially expressed miRNAs (miR-200, miR-122, and miR-205b).

Single-virion sequencing of lamivudinetreated HBV populations reveal population evolution dynamics and demographic history

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Sample identification and collection in the clinic. test single-virion sequencing on biological populations as well as to describe any additional information that can be gained through haplotype sequencing. BAsE-Seq was carried out on all samples. were stopped in the log-linear phase. Insufficient DNA remained from Patients 7 and patient 11 after BAsE-Seq sequencing, and these four samples had to be excluded from Pooled deep sequencing.

Integrated small RNA and Degradome sequencing provide insights into salt tolerance in sesame (Sesamum indicum L.)

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Furthermore, many miRNAs and their target genes have been identi- fied by small RNA and degradome deep sequencing, suggesting that high-throughput sequencing should provide a clear opportunity to identify and validate miRNA–mRNA pairs in plants [18–20]. For instance, one report found that five miRNAs were involved in salt stress response in Hordeum bulbosum using deep se- quencing, and demonstrated their critical roles in better tolerance to salt stress in autopolyploids [21.

A transcriptional landscape of 28 porcine tissues obtained by super deepSAGE sequencing

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Animals, samples collection, and deep sequencing Tissue samples were collected from a private slaughter farm (Jingzhou) located in the Hubei province in China..

Identification and characterization of skin color microRNAs in Koi carp (Cyprinus carpio L.) by Illumina sequencing

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Identification of Koi carp miRNAs via sRNA sequencing To identify miRNAs expressed in the skin of Koi carp, BS, RS, and WS sRNA libraries were determined and analyzed by Illumina deep sequencing. Characterization of miRNAs in different skin tissues To further identify conserved miRNAs and predict novel miRNAs in the three skin color tissues, all sRNA se- quences were mapped to known miRNAs in miRBase.

DCATCH-Seq: Improved sequencing of large continuous genomic targets with doublehybridization

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Targeted sequencing of large genomic regions with CATCH-Seq. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease. Targeted RNA sequencing reveals the deep complexity of the human transcriptome.

Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels

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Best practices for variant calling in clinical sequencing. Evaluation of nine somatic variant callers for detection of somatic mutations in exome and targeted deep sequencing data. Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE et al. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. Narzisi G, O’rawe JA, Iossifov I, Fang H, Lee YH et al. O’Rawe J, Jiang T, Sun G, Wu Y, Wang W et al.

Selective translational usage of TSS and core promoters revealed by translatome sequencing

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Selective translational usage of TSS and core promoters revealed by translatome sequencing. Background: In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Results: In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5 ′ isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution.

De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae)

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De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae). It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. Results: Illumina deep sequencing of the F.

A toolkit for studying Varroa genomics and transcriptomics: Preservation, extraction, and sequencing library preparation

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Population-genomic variation within RNA viruses of the Western honey bee, Apis mellifera, inferred from deep sequencing. Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle. Identification of new viruses specific to the honey bee mite Varroa destructor

High throughput small RNA and transcriptome sequencing reveal capacitation-related microRNAs and mRNA in boar sperm

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In this study, as the first to utilize next generation sequencing for the study of sperm capacitation,we identified and reported differentially expressed mRNA and miRNA profiles in fresh and capacitated boar sperm. Deep sequencing in- formation was obtained to explore the interaction of miRNA and mRNA and to further understand the underlying mechanism of sperm capacitation.. In total, Mirdeep2 detected 1092 unique miRNAs in fresh and capacitated sperm.

Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations

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Back in 1990 the first full genome sequence of the highly-passaged strain AD169 was published based on overlapping PCR amplified fragments, cloning and trad- itional Sanger sequencing [10]. In the era of high throughput sequencing (HTS), dedicated library preparation protocols have been developed to enhance the full genome sequencing of HCMV, based on target enrichment [12], host DNA de- pletion and whole genome amplification [13] or on mul- tiple amplicon deep sequencing [5].

Transcriptome sequencing and whole genome expression profiling of hexaploid sweetpotato under salt stress

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High throughput RNA sequencing is required for identi- fication of candidate genes involved in salt stress toler- ance. In the present study, deep sequencing analyses of PFSP under different durations of salt stress were character- ized as compared to control.