Ontology highlight
ABSTRACT:
PROVIDER: PRJNA896098 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
Project description:Fruit flies Bactrocera melastomatos and B. umbrosa Raw sequence reads
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Project description:Anastrepha (Diptera: Tephritidae) Raw sequence reads
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Project description:Purpose: Cucumber (Cucumis sativus L.) is an economically important vegetable crop worldwide, and cucumber fruit spine density has an important impact on the commercial value. However, little is known about the regulatory mechanism for the fruit spine formation.In this study, the transcriptome analyses of ovaries and pericarps from numerous-spine parent and few-spine parent were conducted to identify the gene regulatory networks involved in the formation and development of numerous fruit spines in cucumber. Methods: Cucumber mRNA profiles of ovaries and pericarps from numerous-spine parent and few-spine parent were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. Then, clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N sequences and low-quality reads from the raw data. Simultaneously, the Q20, Q30 and GC contents of the clean data were calculated. All of the downstream analyses were based on the high-quality clean data. Clean paired-end reads were mapped to the reference genome using TopHat v2.0.12 (Trapnell et al. 2012). Then, the FPKM (fragments per kilobase of transcript sequence per million base pairs sequenced) value of each gene was calculated to estimate gene expression levels (Trapnell et al. 2010). Genes with an adjusted P-value < 0.05 identified by DESeq were assigned as differentially expressed genes(DEGs). Results: We generated 42.96-57.53 million raw reads from each library, and 39.85-54.02 million clean reads were obtained after the removal of low-quality reads and adapter sequences. Among the clean reads, 79.03-80.94% were mapped to the gene database . Based on the KEGG database, pathway enrichment analysis was performed to identify significantly enriched metabolic pathways or signal transduction pathways in DEGs. Plant hormone signal transduction was significantly enriched in up-regulated genes in both F_6DBF compared with M_6DBF and F_0DAA compared with M_0DAA. Conclusions: Based on the transcriptome analysis, we excavated possible biological regulatory networks involved in the formation and development of numerous fruit spines in cucumber. This work will promote the exploration of molecular mechanisms that regulate cucumber fruit spine density.
2018-01-27 | GSE109615 | GEO
Project description:Five novel reference genomes of fruit flies (Diptera, Tephritidae) of agricultural importance in Africa
| PRJNA975840 | ENA
Project description:Background: MicroRNAs (miRNAs) represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Although Hami melon is an attractive model for valuable biological traits analysis, the role of miRNA action in the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the Hami melon miRNA profiles at four fruit developmental stages Results: Small RNA sequencing yielded raw reads in eight libraries. miRNAs expression profiles were variable at different fruit developmental stages. The expression levels of five known miRNAs were validated by quantitative real-time PCR. Among the identified miRNAs, several miRNAs showed developmentally regulated and differentially expressed pattern during fruit development. Conclusions: Our results present a first comprehensive set of identification and characterization of Hami melon fruit miRNAs and their potential targets, which provide valuable basis for further research on the critical role of miRNAs in melon fruit development.
2017-09-06 | GSE77127 | GEO
Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.
2022-09-06 | GSE186354 | GEO
Project description:Two fruit development stages of the wild chiltepin pepper (Capsicum annuum var. glabriusculum) were studied. RNA-Seq data was obtained from fruits at 20 and 68 days after anthesis with two biological replicates for a total of 4 samples. 260 million raw reads were sequenced and over 80% of them mapped back to the Capsicum annuum genome.
2021-08-05 | GSE171889 | GEO
Project description:A cDNA library was constructed by Novogene (CA, USA) using a Small RNA Sample Pre Kit, and Illumina sequencing was conducted according to company workflow, using 20 million reads. Raw data were filtered for quality as determined by reads with a quality score > 5, reads containing N < 10%, no 5' primer contaminants, and reads with a 3' primer and insert tag. The 3' primer sequence was trimmed and reads with a poly A/T/G/C were removed
2021-07-21 | GSE180131 | GEO