SEAweb: The small RNA Expression Atlas on web
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ABSTRACT:
PROVIDER: PRJNA556869 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Small non-coding RNA organ expression atlas
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Project description:Genetic and epigenetic regulations, mostly driven by small non-coding RNAs, play a crucial role to define genetic programming in plant biology and development. In this work, we focus on miRNAs, the most representative class of small RNAs, to present the first comprehensive miRNA expression atlas in Vitis vinifera L. Our atlas gives a clear picture of miRNA regulation and homeostasis in the whole plant during its lifecycle. We analyzed 68 small RNA libraries, which were prepared from a rich and diverse number of tissues (13) harvested on different developmental stages. We identified 110 known miRNAs and annotated 176 novel, some of which belonging to known families and others completely new. We found that very few miRNAs may be defined as tissue specific. However, interestingly, in the stamen 22 miRNAs were found highly specific. Most of the identified miRNAs show low expression levels, whereas, 32 miRNAs are present in all tissues and mainly highly expressed. Additionally, in each organ, the different developmental stages share 30—70% of miRNAs and their modulation leads the regulation of plant development. We also present a target prediction analysis and suggest a first functional description of hundreds of miRNAs. Our findings represent the most complete expression atlas for grapevine and any other woody species, paving the ground for future functional studies. Genome-wide small RNA profiling was done by Illumina TruSeq sample preparation and Illumina Small RNA Sample Prep kit followed by high-throughput sequencing with Illumina HiSeq 2000 and GA IIx Illumina Sequencer platforms for 13 different organs/tissues of grapevine in different developmental stages, with two replicates each, comprising a total of 70 samples
2015-05-01 | E-GEOD-59802 | biostudies-arrayexpress
Project description:We investigate the naturally occurring variation of small RNA expression in conjunction with genetic and gene expression variation. We shall assess the variation in subabdominal fat tissue small RNA levels in 168 unrelated MuTHER individuals. Using gene expression data from the same samples, we can survey how much the small RNA expression contributes to the variance in gene expression profiles. We can also take advantage of the high density genotyping data on these samples to identify genetic associations of small RNA expression levels, and the downstream effect of the genetic variants in small RNA sequence. Previous small RNA sequencing efforts have also extended the repertoire of small RNAs, and we hope to potentially find additional small RNAs active in adipose tissue biology. Altogether, the project should provide an exciting view into small RNA biology in humans, and lead to development of new methodology for analysis of molecular phenotype data.
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Project description:We determine Parkinson’s disease-specific blood biomarker signature using novel data.
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Project description:A mouse tissue atlas of small non-coding RNA
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Project description:Small RNAs, including microRNAs (miRNAs), phased secondary small interfering RNAs (phasiRNA), and heterochromatic small interfering RNAs (hc-siRNA) are an essential component of gene regulation. To establish a broad potato small RNA atlas, we constructed an expression atlas of leaves, flowers, roots, and tubers of Desiree and Eva, which are commercially important potato (Solanum tuberosum) cultivars. All small RNAs identified were observed to be conserved between both cultivars, supporting the hypothesis that small RNAs have a low evolutionary rate and are mostly conserved between lineages. However, we also found that a few miRNAs showed differential accumulation between the two potato cultivars, and that hc-siRNAs have a tissue specific expression. We further identified dozens of reproductive and non-reproductive phasiRNAs originating from coding and noncoding regions that appeared to exhibit tissue-specific expression. Together, this study provides an extensive small RNA profiling of different potato tissues that might be used as a resource for future investigations.
2022-11-11 | GSE213986 | GEO
Project description:Genetic and epigenetic regulations, mostly driven by small non-coding RNAs, play a crucial role to define genetic programming in plant biology and development. In this work, we focus on miRNAs, the most representative class of small RNAs, to present the first comprehensive miRNA expression atlas in Vitis vinifera L. Our atlas gives a clear picture of miRNA regulation and homeostasis in the whole plant during its lifecycle. We analyzed 68 small RNA libraries, which were prepared from a rich and diverse number of tissues (13) harvested on different developmental stages. We identified 110 known miRNAs and annotated 176 novel, some of which belonging to known families and others completely new. We found that very few miRNAs may be defined as tissue specific. However, interestingly, in the stamen 22 miRNAs were found highly specific. Most of the identified miRNAs show low expression levels, whereas, 32 miRNAs are present in all tissues and mainly highly expressed. Additionally, in each organ, the different developmental stages share 30—70% of miRNAs and their modulation leads the regulation of plant development. We also present a target prediction analysis and suggest a first functional description of hundreds of miRNAs. Our findings represent the most complete expression atlas for grapevine and any other woody species, paving the ground for future functional studies.
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Project description:Genotype?Tissue Expression atlas of cattle using 7,180 publicly available RNA-sequencing (RNA-seq) samples
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