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RNA sequencing

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

Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes

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Identification of differentially expressed genes during development of the zebrafish pineal complex using RNA sequencing

Functional module detection through integration of single-cell RNA sequencing data with protein–protein interaction networks

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integration of single-cell RNA sequencing data with protein–protein interaction. Background: Recent advances in single-cell RNA sequencing have allowed researchers to explore transcriptional function at a cellular level. In particular, single-cell RNA sequencing reveals that there exist clusters of cells with similar gene expression profiles, representing different transcriptional states..

Millefy: Visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets

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heterogeneity in read coverage of single-cell RNA sequencing datasets. Background: Read coverage of RNA sequencing data reflects gene expression and RNA processing events.. Single-cell RNA sequencing (scRNA-seq) methods, particularly “full-length” ones, provide read coverage of many individual cells and have the potential to reveal cellular heterogeneity in RNA transcription and processing.

A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded samples

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The quality of the RNA samples from the fifteen clinical samples. Comparison of four RNA library preparation kits for FFPE samples. The consistency of transcript quantification of four RNA library preparation kits with FFPE samples. Comparison of mapping data using HISAT and STAR in FF and FFPE samples. RNA-seq: RNA sequencing. Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples.

The effect of methanol fixation on singlecell RNA sequencing data

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The effect of methanol fixation on single- cell RNA sequencing data. Results: We adapted an existing methanol fixation protocol and performed scRNA-seq on both live and methanol fixed cells. In this study, we comprehensively evalu- ated the effect of methanol fixation on single-cell RNA- seq results. We performed the analysis at gene and tran- script levels and observed both similarities and inconsist- encies between the transcriptomic profiles of live and fixed cells.

Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

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The bootstrap values (marked by parentheses) were in the format for displaying percentages with. sRNA-seq: small RNA sequencing. SB and SK contributed to subsequent drafts of the manuscript.. The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript..

Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion

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EMBR-seq allows mRNA sequencing from low input total RNA. In many practical applications involving non-model and non-cultivable bacterial species, the starting amount of total RNA available for RNA sequencing can be limiting.. We applied EMBR-seq to and 0.02 ng of starting total RNA isolated from the ex- ponential growth phase of E.

A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis

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Illumina RNA sequencing. Analysis of the DEGs. Between 14 DAF and 21 DAF were 3930 and 3877, respectively. A total of 685 up- and 335 down- regulated DEGs were identified among 7 DAF, 14 DAF and 21 DAF (Fig.

Analysis of histology and long noncoding RNAs involved in the rabbit hair follicle density using RNA sequencing

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Integrated analysis of the roles of long noncoding RNA and coding RNA expression in sheep (Ovis aries) skin during initiation of secondary hair follicle. Systematic analysis of non-coding RNAs involved in the angora rabbit (Oryctolagus cuniculus) hair follicle cycle by RNA sequencing. The functions of ocu-miR-205 in regulating hair follicle development in Rex rabbits. Variation in the caprine keratin-associated protein 15-1 (KAP15-1) gene affects cashmere fibre diameter.

A comparison between whole transcript and 3’ RNA sequencing methods using Kapa and Lexogen library preparation methods

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Trad-KAPA detects more differentially expressed genes One major application of RNA sequencing is the identifi- cation of differentially expressed genes (DEGs).

Identification of diverse cell populations in skeletal muscles and biomarkers for intramuscular fat of chicken by single-cell RNA sequencing

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KEGG enrichment pathways and related genes in Cluster 2 at D5. scRNA-seq: Single-cell RNA Sequencing. Wei Li (Institute of Animal Sciences of Chinese Academy of Agriculture Sciences, Beijing, China) for assistance in the cell extraction.. All authors have read and agreed to the published version of the manuscript.. The single-cell RNA sequencing clean data reported in this paper have been deposited in the Genome Sequence Archive [38] in BIG Data Center [39].

Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing

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Gene expression response to sea lice in Atlantic salmon skin: RNA sequencing comparison between resistant and susceptible animals. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118

Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.)

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Here, small RNA sequencing was performed in the stems from the pre-elongation stage, early elongation stage and rapid elongation stage in the present study. Subsequently, the miRNAs involved in control of the gene expression that was related to internode elongation was analyzed. and “plant hormone signal transduction” pathways par- ticipated in sugarcane internode elongation. In the.

Comparative evaluation for the globin gene depletion methods for mRNA sequencing using the whole blood-derived total RNAs

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Thus, the probe hybridization depletion is an appropri- ate method for the mRNA sequencing that is both. In this study, we showed 1 μg of high-quality RNA from whole blood collected in PAXgene Blood RNA tubes may be routinely used for transcriptional profiling ana- lysis studies. In addition, we have demonstrated that the probe hybridization depletion method is more suited to mRNA sequencing analysis with minimal effect on RNA quality during depletion procedures from whole blood- derived RNA.

Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing

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In parallel, head kidney and liver samples were taken from animals of the same population with high and low genomic breeding values for resistance, and used for RNA-Sequencing to compare their transcriptome profile both pre and post infection.. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/..

RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge

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The RNA Sequencing dataset supporting the conclusions of this article are available in the NCBI GEO database under accession number GSE148588 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148588).

Strategies for detecting and identifying biological signals amidst the variation commonly found in RNA sequencing data

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RNA sequencing counts routinely display large differ- ences in their relative gene expression levels, which scales with the mean of the sequenced counts. In our Control sample, MVA of the 8746 genes reduced the mean and standard deviation by an average of 3.9-fold.

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

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RNA sequencing of the heart of 16 infected (7 and 14 days post infection) and 8 control fish highlighted 4927 and 2437 differentially expressed genes at 7 and 14 days post infection respectively. Comparison of the transcriptomic response of fish with high and low breeding values for resistance highlighted TRIM25 as being up-regulated in resistant fish..

Identification and characterization of long noncoding RNAs and mRNAs expression profiles related to postnatal liver maturation of breeder roosters using Ribozero RNA sequencing

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Developmental changes of protein-coding genes and lncRNAs in postnatal liver development of chicken We gathered 1570 differentially expressed mRNAs be- tween immature and mature livers meeting the criteria Table 1 Statistical data of the RNA-Sequencing reads for six samples. 1 Characteristics of lncRNAs in the livers of chickens (Gallus gallus). In addition, 214 differentially expressed lncRNAs between immature and mature livers meeting the criteria of P <.

Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops

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Conclusions: RNA-sequencing-based analyses successfully evaluated genome differentiation among the diploid Triticum and Aegilops species and supported the chromosome-pairing-based genome nomenclature system, except for the position of Ae. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. Full list of author information is available at the end of the article.