Small RNA identification in Arabidopsis thaliana using modified MPSS
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE3008 | GEO | 2005/09/02
SECONDARY ACCESSION(S): PRJNA93187
REPOSITORIES: GEO
Similar Datasets
Project description:Small RNAs play important regulatory roles in most eukaryotes but only a small proportion of these molecules have been identified. We sequenced more than two million small RNAs from seedlings and the inflorescence of the model plant Arabidopsis thaliana. Known and new miRNAs were among the most abundant of the non-redundant set of more than 75,000 sequences, whereas more than half represented lower abundance small-interfering RNAs (siRNAs) that match repetitive sequences, intergenic regions, and genes. Individual or clusters of highly-regulated small RNAs were readily observed. Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs. Small RNAs identified in seedlings and inflorescence tissues.
2005-09-02 | E-GEOD-3008 | biostudies-arrayexpress
Project description:A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms. Here, different Treatments/Conditions based on different Arabidopsis tissues were used for three different platforms include MPSS, Affymetrix and Agilent. Keywords: MPSS, Affymetrix, Agilent For the comparison, 11 different samples were used: Callus, Inforescence, Leaf, Root, Silique, Afamous Inflorescence, Ap1-10 Inflorescence, Ap3-6 Inflorescence, Sup/Ap1 Inflorescence, Leaves SA 4 hr and Leaves SA 52 hr. For details about samples, see Meyers Lab (http://mpss.udel.edu/at). All RNA samples were created in Meyers Lab. MPSS experiments were performed in Meyers Lab. Affymetrix experiments were performed in St. Clair Lab (http://stclairlab.ucdavis.edu/). Agilent experiments were performed by Sean J Coughlan from Agilent (http://www.agilent.com/). Two replicates for each samples were used in Affymetrix platform except Silique sample. Two replicates for each samples were used in Agilent platform.
2007-09-14 | E-GEOD-8994 | biostudies-arrayexpress
Project description:The Arabidopsis genome contains a highly complex and abundant population of small RNAs, and many of the endogenous siRNAs are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. By analyzing an rdr2 loss-of-function mutant using two different parallel sequencing technologies, MPSS and 454, we characterized the complement of miRNAs expressed in Arabidopsis inflorescence to considerable depth. Nearly all known miRNAs were enriched in this mutant and we identified 13 new miRNAs, all of which were relatively low abundance and constitute new families. Trans-acting siRNAs (ta-siRNAs) were even more highly enriched. Computational and gel blot analyses suggested that the minimal number of miRNAs in Arabidopsis is approximately 155. The size profile of small RNAs in rdr2 reflected enrichment of 21-nt miRNAs and other classes of siRNAs like ta-siRNAs, and a significant reduction in 24-nt heterochromatic siRNAs. Other classes of small RNAs were found to be RDR2-independent, particularly those derived from long inverted repeats and a subset of tandem repeats. The small RNA populations in other Arabidopsis small RNA biogenesis mutants were also examined; a dcl2/3/4 triple mutant showed a similar pattern to rdr2, whereas dcl1-7 and rdr6 showed reductions in miRNAs and ta-siRNAs consistent with their activities in the biogenesis of these types of small RNAs. Deep sequencing of mutants provides a genetic approach for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs. Keywords: small RNA sequences generated by 454 sequencing
2006-09-08 | GSE5343 | GEO
Project description:Identification of all expressed transcripts in a sequenced complex genome is technically challenging, but essential for systems biology and genome analysis. We used the transcriptional profiling technology called ‘massively parallel signature sequencing’ (MPSS) to develop a comprehensive expression atlas of rice (Oryza sativa cv Nipponbare). A total of 46,971,553 mRNA transcripts from 22 libraries, and 2,953,855 small RNAs from three libraries were sequenced. The data demonstrated widespread transcription throughout the genome, including expression for up to 25,500 annotated genes and antisense expression for nearly 9,000 annotated genes. An additional set of ~15,000 mRNA signatures mapped to unannotated genomic regions. The majority of the small RNA data represented lower abundance small-interfering RNAs (siRNAs) that match repetitive sequences, intergenic regions, and genes. Among these, numerous clusters of highly-regulated small RNAs were readily observed. We developed a genome browser (http://mpss.udel.edu/rice) for public access to the transcriptional profiling data for this important crop plant. Keywords: MPSS, mRNA, small RNA, transcriptome, rice
2007-02-23 | GSE7107 | GEO
Project description:MPSS mouse transcriptome analysis project. See http://www.ncbi.nlm.nih.gov/geo/info/mouse-trans.html for more details. Keywords: other
2004-10-26 | GSE1581 | GEO
Project description:Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ~240 miRNAs have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes. Among these, we found a novel class of miRNAs that derive from natural cis-antisense transcript pairs. This configuration generates miRNAs that can perfectly match their targets. We provide evidence that the miRNAs function by inducing mRNA cleavage in the middle of their complementary site. Their production requires DCL1 activity, which is essential for canonical miRNA biogenesis. All of the nat-miRNAs identified in this study have large introns in their precursors that appear critical for nat-miRNA evolution and for the formation of functional miRNA loci. These findings suggest that other natural cis-antisense loci with similar exon-intron arrangements could be another source of miRNA genes Keywords: small RNA sequencing by MPSS
2008-02-15 | GSE10523 | GEO
Project description:The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most muticellular eukaryotes, centromeres are composed of long tracks of satellite repeats that are recalcitrant to sequencing and fine scale genetic mapping. Here we report the genomic and genetic characterization of the complete centromere of rice chromosome 3. Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains ~414 kb of the centromeric satellite repeat CentO. Cen3 includes a ~1,851-kb domain associated with CENH3, the centromere-specific histone H3 variant. This CENH3-associated chromatin domain is embedded within a 3,083-kb region that lacks genetic recombination. We detected several active genes within the CENH3-binding domain based on a comprehensive annotation and a survey for matches with mRNA signatures. However, the gene density in the CENH3-binding domain is significantly lower than in the pericentromeric domains. In contrast, the CENH3-binding domain contains a higher percentage of repetitive DNA sequences than the pericentromeric regions. These results suggest that Cen3 is in the process of evolving from a genic region toward an accumulation of satellite repeats and transposable elements that is more characteristic of centromeres in most complex eukaryotic species. MPSS was performed to sequence small RNAs that derived from inflorescence and seedling. The method for the MPSS sequencing of small RNAs are described in the paper associated with this dataset (Lu et al., 2005).
2006-05-26 | E-GEOD-4912 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Hordeum vulgare tissues (leaves, inflorescence and leaves inoculated with Blumeria). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.
2011-05-10 | GSE28966 | GEO
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Hordeum vulgare tissues (leaves, inflorescence and leaves inoculated with Blumeria). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, inflorescence and leaves inoculated with Blumeria of Hordeum vulgare. Each tissue represented a mixture of developmental stages. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Roger Wise for providing the plant material and Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods..
2011-05-09 | E-GEOD-28966 | biostudies-arrayexpress
Project description:This series represents a very deep survey of all transcripts expressed in a wide range of human tissues and cells by Massively Parallel Signature Sequencing (MPSS). These datasets have been generated and donated to the scientific community by Lynx Therapeutics, Inc in Hayward, CA. The data contained in this submission is described in the following publication: 'C. Victor Jongeneel, Mauro Delorenzi, Christian Iseli, Daixing Zhou, Christian D. Haudenschild, Brian J. Stevenson, Robert L. Strausberg, Andrew J.G. Simpson, and Thomas J. Vasicek.' An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Research VolXX 2004 Abstract of the publication: 'We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of over 20,000 genes with high sensitivity and specificity. The data confirm the widely held belief that differences between cell and tissue types are largely determined by the expression of a limited number of tissue-specific genes, rather than by combinations of more promiscuously expressed genes. Expression of a little over half of all known human genes seems to account for both the common requirements and the specific functions of the tissues sampled. A classification of tissues based on patterns of gene expression largely reproduces classifications based on anatomical and biochemical properties. The unbiased sampling of the human transcriptome achieved by MPSS supports the notion that most human genes have been mapped, if not functionally characterised. This dataset should prove useful for the identification of tissue-specific genes, for the study of global changes induced by pathological conditions, and for the definition of a minimal set of genes necessary for basic cell maintenance.' Keywords: other
2005-11-29 | GSE1747 | GEO