A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE7233
PROVIDER: PRJNA97913 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequence-complementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents that were enriched in neuronal as well as normal and malignant hematopoietic cells and tissues. We present expression profiles derived from clone count data and provide computational tools for their analysis. Unexpectedly, a relatively small set of miRNAs, many of which are ubiquitously expressed, account for most of the differences in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units, and conservation patterns. We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses.
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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:MicroRNAs (miRNAs) are small non-coding regulatory RNAs that reduce stability and/or translation of fully or partially sequence-complementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents, enriched in euronal as well as normal and malignant hematopoietic cells and tissues. We present expression profiles derived from clone count data and provide novel computational tools for their analysis. Unexpectedly, a relatively small set of miRNAs, many of which are ubiquitously expressed, account for most of the difference in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units and conservation patterns. We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses. Keywords: miRNA microarray; expression profiling
2007-06-17 | GSE7233 | 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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2020-07-19 | GSE134671 | GEO
Project description:Nanobody is one special type of single-domain antibody fragment with multiple advantages over traditional antibody. Our previous work established linear-double-stranded DNA (ldsDNA, or PCR amplicon) as novel biological parts for building AND gate genetic circuits in mammalian cells. During this AND-gate circuit formation process, the co-transfected up- and down-stream ldsDNAs could be linked together to form intact gene expression cassette. Here, we employed this ldsDNA-based AND-gate (LBAG) strategy to construct nanobody library in mammalian cells. The sequence complexity of complementary determining regions (CDRs) was introduced into ldsDNA by PCR amplification. After being co-transfected into mammalian cells, the up- and down- stream ldsDNAs undergo AND gate linkage and form full nanobody coding regions, containing CDR1-3. High throughput sequencing identified 22,173 unique oligonucleotide sequences in total generated by this strategy. Thus, we developed a novel method to construct nanobody library, which is a start point for building high content nanobody library in mammalian cells.
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2023-10-05 | GSE226719 | GEO
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| PRJNA666932 | ENA