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Small RNA

Tìm thấy 16+ kết quả cho từ khóa "Small RNA"

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..

Genome-wide small RNA profiling reveals tiller development in tall fescue (Festuca arundinacea Schreb)

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In our previous work, we carried out transcriptome analysis in tall fescue and small RNA analysis and identified. Both RNA-Seq and small RNA analyses provided rich information for the understanding of the molecular mechanism of tiller- ing development or heat stress response in tall fescue.. Here, we identified 18 miRNAs involved in tall fescue tiller development.

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.

Different classes of small RNAs are essential for head regeneration in the planarian Dugesia japonica

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Conclusions: Our findings suggest that a complex pool of small RNAs takes part in the process of head regeneration in Dugesia japonica and provide novel insights into global small RNA expression profiles and expression changes in response to head amputation.

Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions

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VK carried out most of the experiments and supported RNA sequencing data analysis. The small RNA-seq data has been submitted to the National Center for Bio- technology Information (NCBI) Gene expression Omnibus (GEO) with acces- sion number GSE117764.. Small RNAs of the Bradyrhizobium/ Rhodopseudomonas lineage and their analysis.. Independent activity of the homologous small regulatory RNAs AbcR1 and AbcR2 in the legume symbiont Sinorhizobium meliloti.

Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce

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Landscape of fluid sets of hairpin-derived 21 − /24-nt- long small RNAs at seed set uncovers special epigenetic features in Picea glauca. 24-nt reproductive phasiRNAs are broadly present in angiosperms. Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development

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

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Small RNA sequencing and annotation of sesame miRNAs In the study, 18 small RNA libraries of ST and SS geno- types under control and salt stress conditions (12 and 24 h) were constructed and sequenced. 351 conserved/known miRNAs were identified in sesame. Differential expression of miRNAs under salt stress In this study, a total of 116 differentially expressed miR- NAs were identified in the two sesame accessions under salt stress.

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

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Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs.

RNA isolation from cell free – Saliva of water buffalo

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Because of cell free saliva, traces of ribosomal RNA and large fragmental RNA were not included in the RNA sample. The treatment of 1/10 th volume 8M lithium chloride to the aqueous phase may also be responsible for enrichment of small RNA in the form of pellet and separation of larger fragmental RNA collected into the supernatant (Prasanta et al.

Identification of oligo-adenylated small RNAs in the parasite Entamoeba and a potential role for small RNA control

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There is a prominent peak at 27 nt and a very small peak at 21 nt in the EhAgo2–3 IP library, indicating the smaller 21 nt RNA band was not cloned efficiently (as expected, likely because of their 5′-OH structure).. As the sRNAs bound to EhAgo2–2 have a G bias in the 5′-nucleotide position [21, 22], we checked the nu- cleotide composition of sRNAs in the EhAgo2–1 and EhAgo2–3 IP libraries.

The micro-RNA content of unsorted cryopreserved bovine sperm and its relation to the fertility of sperm after sexsorting

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EK performed the lab work (total RNA extraction and quality control, preparation of small RNA libraries), carried out part of the bioinformatic analysis, reviewed the existing literature and prepared the manuscript. SiB carried out part of the lab work (total RNA extraction and quality control, preparation of small RNA libraries). SW and UW contributed to the conception of the work, the collection of the samples and fertility data.

Environmental RNAi pathways in the twospotted spider mite

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Column enrichment of small RNA containing complexes used 1 mL HiTrap Q FF columns (GE Lifesciences) as previously described [20]. RNA obtained from both column extraction and total RNA extraction were sequenced from an Illumina True- Seq Small RNA Library Prep Kit library. Small RNA TruSeq libraries were initially processed using Fastx toolkit to remove adapter sequences [33].

In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1

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Structural characterization of the RNA chaperone Hfq from the nitrogen-fixing bacterium Herbaspirillum seropedicae SmR1.. Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome. The role of ribonucleases and sRNAs in the virulence of foodborne pathogens. The critical role of RNA processing and degradation in the control of gene expression. The crucial role of PNPase in the degradation of small RNAs that are not associated with Hfq.

Identification of miRNA-eQTLs in maize mature leaf by GWAS

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For developing small RNA libraries through the NEB small RNA library prep kit, a 2 ng fraction of the total RNA of each sample from 282 maize lines was prepared and shipped to the company “Global Biologics”. Library analysis and estimation of miRNA expression A total of 200 out of the original 282 libraries derived from mature leaf samples were selected based on the quality of sequencing, and reads with lengths between 20 and 32 bp were kept after trimming the adapter..

Phytohormone and integrated mRNA and miRNA transcriptome analyses and differentiation of male between hermaphroditic floral buds of andromonoecious Diospyros kaki Thunb

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Twelve small RNA libraries at stages 2 (MA1, MA2, and MA3 for the male and HA1, HA2, and HA3 for the hermaphroditic) and 4 (MB1, MB2, and MB3 for the male and HB1, HB2, and HB3 for the hermaphroditic) were constructed with total RNA and sequenced on the BGISEQ-500 platform to investigate miRNA differenti- ation between the male and hermaphroditic floral buds..

Investigation of the host transcriptional response to intracellular bacterial infection using Dictyostelium discoideum as a host model

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The small RNA repertoire of Dictyostelium discoideum and its regulation by components of the RNAi pathway. MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs. characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum. Analysis of the microprocessor in Dictyostelium: the role of RbdB, a dsRNA binding protein.

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

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EMBR-seq effectively depletes rRNA from frag- mented total RNA. Combining TerminatorTM 5 ′ -phosphate- dependent exonuclease (TEX) digestion with EMBR-seq does not improve rRNA depletion. Cost associated with performing EMBR-seq. Higher number of genes detected in EMBR-seq is not dependent on the sequencing depth. coli op- erons in EMBR-seq. Gene transcript count correlation between different input total RNA amounts in EMBR-seq. Single-cell sequencing of the small-RNA transcriptome

Genome-wide miRNA analysis and integrated network for flavonoid biosynthesis in Osmanthus fragrans

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Small RNA discovery in the interaction between barley and the powdery mildew pathogen

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments

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In general, pooling RNA samples or pooling RNA samples in conjunction with moderate reduction of the sequencing depth can be good options to optimize the cost and maintain the power.. Full list of author information is available at the end of the article. The number of biological repli- cates in an RNA-seq experiment is typically small because of financial or technical constraints. For RNA-seq data, Rajkumar et al.

Temporal changes in DNA methylation and RNA expression in a small song bird: Within- and between-tissue comparisons

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Temporal changes in DNA methylation and RNA expression in a small song bird:. Background: DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of DNA methylation we need simultaneous within-individual assessment of methylation changes and gene expression changes over time.