Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1197143 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31731930.fastq.gz | Fastqsanger.gz | |||
| SRR31731931.fastq.gz | Fastqsanger.gz | |||
| SRR31731932.fastq.gz | Fastqsanger.gz | |||
| SRR31731933.fastq.gz | Fastqsanger.gz | |||
| SRR31731934.fastq.gz | Fastqsanger.gz |
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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 Ginkgo biloba tissues (leaves, female and male cones). 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, female and male cones of Ginkgo biloba. 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 Eric Brenner for providing the plant material and Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods..
2011-05-09 | E-GEOD-28963 | biostudies-arrayexpress
Project description:To explore the overall long noncoding RNA (lncRNA) involved in major developmental stages of Ginkgo biloba leaves , we deeply sequenced samples of leaves from different developmental stages (from April to October) using strand-specific RNA sequencing (ssRNA-seq) menthod. We obtained 27.44 Gb raw data and identified 1323 novel lncRNAs. We also categorized the novel lncRNAs as intergenic, intronic, antisense and sense based on their location on theGinkgo biloba genome. Furthermore, lncRNAs targeted protein-coding genes were predicted and functional annotated. In addition, we constructed a network of interactions between ncRNAs (miRNAs, lncRNA) and mRNAs. Our results suggest that the identified novel lncRNAs are important in modulating development process of Ginkgo biloba, and provide a rich resource for further research on the function of these novel lncRNAs.
2018-05-01 | GSE109917 | 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 Ginkgo biloba tissues (leaves, female and male cones). 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 | GSE28963 | GEO
Project description:We sequenced mRNA from the leaves of mutant and normal green leaves of Ginkgo biloba using the Illumina HiSeq4000 platform to generate the transcriptome dynamics that may serve as a gene expression profile blueprint for leaf color variation of the mutant in Ginkgo biloba.
2017-11-01 | GSE103827 | GEO
Project description:We conducted RNA-seq from the Ginkgo leaves after UV-B treatment,and constructed the molecular regulatory network of flavonoids synthesis under UV-B radiation in G. biloba.
2019-12-13 | GSE141890 | GEO
Project description:We sequenced mRNA from Ginkgo biloba leaves grown at different developmental stages using the Illumina HiSeq4000 platform to generate the transcriptome dynamics that may serve as a gene expression profile blueprint for different response patterns during autumn leaf senescence and coloration. These results contribute to the elucidation of the molecular mechanisms involved in the leaf coloration and senescence in G. biloba as well as to the identification of candidate genes involved in this process.
2019-10-19 | GSE139096 | GEO
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
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