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    Results: 20

    1.

    Massive analysis of rice small RNAs: Mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage

    (Submitter supplied) Small RNAs have variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify novel and regulated rice miRNAs, 62 small RNA libraries were constructed from rice plants and deeply sequenced with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. more...
    Organism:
    Oryza sativa
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platforms:
    GPL9147 GPL9316
    62 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE32973
    ID:
    200032973
    2.

    A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains

    (Submitter supplied) Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as posttranscriptional or transcriptional regulators in plants. miRNA function is essential for normal development and therefore likely to be important in the growth of the rice grain. To investigate the likely roles of miRNAs in rice grain development we carried out deep sequencing of the small RNA populations of rice grains. more...
    Organism:
    Oryza sativa
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platforms:
    GPL9147 GPL9388
    6 Samples
    Download data:
    GEO (FNA, QUAL, TXT), SRA SRP007800
    Series
    Accession:
    GSE11014
    ID:
    200011014
    3.

    Uncovering small RNA-mediated responses to phosphate-deficiency in Arabidopsis by deep sequencing

    (Submitter supplied) Deep sequencing of Arabidopsis thaliana small RNAs was conducted to reveal microRNAs (miRNAs) and other small RNAs that were differentially expressed in response to phosphate (Pi) deficiency. About 3.5 million sequence reads corresponding to 0.6-1.2 million unique sequence tags from each Pi-sufficient or -deficient root or shoot sample were mapped to the Arabidopsis genome. We showed that upon Pi deprivation, the expression of miR156, miR399, miR778 and miR827 was induced, whereas the expression of miR169, miR395 and miR398 was repressed. more...
    Organism:
    Arabidopsis thaliana
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL9062
    4 Samples
    Download data:
    GEO, SRA SRP001557
    Series
    Accession:
    GSE17741
    ID:
    200017741
    4.

    Transcriptome-wide identification of small RNA targets in rice

    (Submitter supplied) MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. Most miRNA targets in Arabidopsis are validated, but those in rice are yet to be characterized. To identify transcriptome-wide small RNA targets in rice, we generated 20-nt small cDNA library and obtained nearly 40 million reads. more...
    Organism:
    Oryza sativa
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL9147
    1 Sample
    Download data:
    GEO (TXT), SRA SRP002288
    Series
    Accession:
    GSE17398
    ID:
    200017398
    5.

    High-throughput sequencing of small RNA transcriptome reveals salt stressed regulated microRNAs in sugarcane

    (Submitter supplied) Salt stress is a primary cause of crop losses worldwide, and it has been the subject of intense investigation to unravel the complex mechanisms responsible for salinity tolerance. MicroRNA is implicated in many developmental processes and in responses to various abiotic stresses, playing pivotal roles in plant adaptation. Deep sequencing technology was chosen to determine the small RNA transcriptome of Saccharum sp cultivars grown on saline conditions. more...
    Organism:
    Saccharum hybrid cultivar SP70-1143
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL16317
    4 Samples
    Download data:
    GEO (TXT), SRA SRP017293
    Series
    Accession:
    GSE42484
    ID:
    200042484
    6.

    Roles of RDR701 and DCLs in Rice PhasiRNA biogenesis

    (Submitter supplied) In this study, we analyzed function of the rice RDR701 and various DCLs proteins in small RNA processing. small RNA deep sequencing analyses revealed that RDR701 and OsDCL4 is involved in tasiRNAs and 21- and 24-nt phasiRNAs biogenesis. Further analyses indicate RDR701 coupling with OsDCL4 and OsDCL3b are required for the biogenesis of 21- and 24-nt phasiRNAs, respectively. The triggering miRNAs for intial both size phasiRNAs,are also shown RDR701- and OsDCL4-dependent, suggesting two sequential round activity of RDR701 in associated with different DCLs are essential for rice phasiRNAs biogenesis.
    Organism:
    Oryza sativa
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL9147
    4 Samples
    Download data:
    GEO, SRA SRP005146
    Series
    Accession:
    GSE26405
    ID:
    200026405
    7.

    Small RNA Solexa sequencing of 4 Plant Species in the Cucurbitaceae family

    (Submitter supplied) Total RNA was isolated from different tissues (leaf, stem and flesh, rind and placenta of the fruits) using TRIzol reagent and small RNA libraries were generated from four cucurbit species: bottle gourd (Lagenaria siceraria (accession Grif 1617 collection from India)), Cucurbita moschata (accession Grif 14244 Early Butternut) Cucurbita pepo (accession NSL98075 Table King), and watermelon (Citrullus lanatus var. more...
    Organism:
    Citrullus lanatus subsp. vulgaris; Lagenaria siceraria; Cucurbita pepo; Cucurbita moschata
    Type:
    Non-coding RNA profiling by high throughput sequencing
    4 related Platforms
    4 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE38176
    ID:
    200038176
    8.

    Genome-wide profiling of miRNAs and their target genes during somatic embryogenesis in cotton by small RNA and degradome sequencing

    (Submitter supplied) MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide (nt) RNAs that regulate gene expression at transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress responses or pathogen responses. miRNAs with their related target genes have been widely studied in model plants,and increasing studies have been performed on some crops,however, the number of identified miRNAs in cotton was limited, and global identification of related targets through degradome sequencing has not been developed previously. more...
    Organism:
    Gossypium hirsutum
    Type:
    Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL16101
    4 Samples
    Download data:
    GEO (TXT), SRA SRP015881
    Series
    Accession:
    GSE41132
    ID:
    200041132
    9.

    Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male sterile line by deep sequencing (Degradome-Seq)

    (Submitter supplied) The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. more...
    Organism:
    Triticum aestivum
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL10467
    2 Samples
    Download data:
    GEO (TXT), SRA SRP012140
    Series
    Accession:
    GSE37134
    ID:
    200037134
    10.

    Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male sterile line by deep sequencing

    (Submitter supplied) The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. more...
    Organism:
    Triticum aestivum
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL10467
    7 Samples
    Download data:
    GEO (TXT), SRA SRP011979
    Series
    Accession:
    GSE36867
    ID:
    200036867
    11.

    Divergent Patterns of Endogenous Small RNA Populations From Seed and Vegetative Tissues of Glycine max

    (Submitter supplied) An overview of small RNAs sequences existing in seed development and contrasted with vegetative tissues of the soybean
    Organism:
    Glycine max
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL10267
    4 Samples
    Download data:
    GEO (TXT), SRA SRP011915
    Series
    Accession:
    GSE36728
    ID:
    200036728
    12.

    Comprehensive investigation of miRNAs enhanced by analysis of sequence variants, expression patterns, AGO loading and target cleavage

    (Submitter supplied) MicroRNAs (miRNAs) are a class of small RNAs which typically function by guiding cleavage of target messenger RNAs. They have been shown to play major roles in a variety of plant processes including development, and responses to pathogens and environmental stresses. To identify new miRNAs and regulation in Arabidopsis thaliana, 27 small RNA libraries were constructed and sequenced from various tissues, stresses and small RNA biogenesis mutants, resulting in 95 million genome-matched sequences. more...
    Organism:
    Arabidopsis thaliana
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL9302
    27 Samples
    Download data:
    GEO (TXT), SRA SRP018840
    Series
    Accession:
    GSE44622
    ID:
    200044622
    13.

    Expression profiling of small RNAs in control and H2O2-treated rice seedlings

    (Submitter supplied) We aimed to identify putative H2O2-regulated miRNAs expressed in rice seedlings under oxidative stress by using a deep sequencing approach developed by Solexa (Illumina). Two small RNA libraries were constructed from H2O2-treated and control rice seedlings, and more than five million small RNA sequence reads were generated for each library. We identified seven H2O2-responsive miRNA families via expression profiling of the miRNAs based on a comparative miRNAomic analysis in combination with experimental validation. more...
    Organism:
    Oryza sativa
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL9147
    2 Samples
    Download data:
    GEO, SRA SRP003156
    Series
    Accession:
    GSE23217
    ID:
    200023217
    14.

    Identification and Analysis of Red Sea Mangrove (Avicennia marina) microRNAs by High-Throughput Sequencing and their Association with Stress Responses

    (Submitter supplied) we used high-throughput Illumina Genome Analyzer IIx (GAIIx) technology to sequence the small RNA transcriptomes of the mangrove species, Avicennia marina. Based on sequence similarity or the secondary structure of precursors, we have identified 193 conserved miRNAs and 26 novel miRNAs in the small RNA transcriptome of Avicennia marina.
    Organism:
    Avicennia marina
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL16535
    1 Sample
    Download data:
    GEO (TXT), SRA SRP018103
    Series
    Accession:
    GSE43669
    ID:
    200043669
    15.

    Genomic dissection of small RNAs in wild rice (O.rufipogon): lessons for rice domestication [degradome]

    (Submitter supplied) The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. more...
    Organism:
    Oryza rufipogon
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL10246
    1 Sample
    Download data:
    GEO (FA), SRA SRP014309
    Series
    Accession:
    GSE39307
    ID:
    200039307
    16.

    Identification of soybean seed developmental stage specific and tissue specific miRNA targets by degradome sequencing .

    (Submitter supplied) Five degradome libraries were constructed from three different seed developmental stages. Separate degradome libraries were constructed for seed coat and cotyledons to identify the tissue specific miRNAs and their potential targets. Sequencing and analysis of degradome libraries gives identification of 183 different targets for 80 known soybean miRNAs. We found 30 cotyledon specific, 18 seed coat specific and 32 miRNAs found in both tissues irrespective of the developmental stages. more...
    Organism:
    Glycine max
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL15008
    5 Samples
    Download data:
    GEO (TXT), SRA SRP009822
    Series
    Accession:
    GSE34433
    ID:
    200034433
    17.

    Expression data from rice leaves treated or not with fungal elicitors and high-throughput pyrosequencing of endogenous small RNAs from Oryza sativa

    (Submitter supplied) High-throughput sequencing of small RNAs from rice was used to identify distinct miRNAs that are responsive to elicitors from the fungal pathogen Magnaporthe oryzae. [Expression profiling by array] We used microarrays to determine the expression behaviour of target genes for elicitor-regulated miRNAs. [High throughput sequencing] High-throughput sequencing of rice small RNAs was performed in two different tissues, leaves and roots, and two different time point of elicitor treatment, 30' and 2h Amplicons were prepared by 5´and 3´adaptor ligation in which the 5'-adaptor contained a 'barcode' consisting of a 4-nucleotide identifier sequence for each sample. more...
    Organism:
    Oryza sativa; Oryza sativa Japonica Group
    Type:
    Expression profiling by array; Non-coding RNA profiling by high throughput sequencing
    Platforms:
    GPL13925 GPL2025
    20 Samples
    Download data:
    GEO (CEL, FASTA), SRA SRP007531
    Series
    Accession:
    GSE30583
    ID:
    200030583
    18.

    Differentiated Truncation and Uridylation Patterns of miRNAs in Arabidopsis and Rice hen1 Mutants Suggest miRNAs May Re-program RISC

    (Submitter supplied) miRNA levels depend on both biogenesis and turnover. The methyltransferase HEN1 stabilizes plant miRNAs, animal piRNAs, and siRNAs in both kingdoms via 3' terminal methylation. Loss of HEN1 in plants results in non-templated oligo-uridylation and accelerated degradation of miRNAs. In hen1 mutants from Arabidopsis and rice, we found that the patterns of miRNA truncation and uridylation differ substantially among miRNA families, but such patterns for the same miRNA are conserved between species. more...
    Organism:
    Oryza sativa; Zea mays; Arabidopsis thaliana
    Type:
    Non-coding RNA profiling by high throughput sequencing
    4 related Platforms
    33 Samples
    Download data:
    GEO (TXT), SRA SRP010770
    Series
    Accession:
    GSE35562
    ID:
    200035562
    19.

    Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice

    (Submitter supplied) Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. more...
    Organism:
    Oryza sativa
    Type:
    Expression profiling by array
    Platform:
    GPL2025
    36 Samples
    Download data:
    GEO (CEL)
    Series
    Accession:
    GSE26280
    ID:
    200026280
    20.

    Identification of miRNAs and their target genes in developing seeds of soybean by deep sequencing

    (Submitter supplied) In our study, small RNA library and degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis, and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. more...
    Organism:
    Glycine max
    Type:
    Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
    Platform:
    GPL11192
    2 Samples
    Download data:
    GEO (TXT), SRA SRP004444
    Series
    Accession:
    GSE25260
    ID:
    200025260

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