Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1126169 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29524934_1.fastq.gz | Fastqsanger.gz | |||
| SRR29524934_2.fastq.gz | Fastqsanger.gz | |||
| SRR29524935_1.fastq.gz | Fastqsanger.gz | |||
| SRR29524935_2.fastq.gz | Fastqsanger.gz | |||
| SRR29524936_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
Similar Datasets
Project description:Two complementary protein extraction methodologies coupled with an automated proteomic platform were employed to analyze tissue-specific proteomes and characterize biological and metabolic processes in sweet potato. A total of 74,255 peptides corresponding to 4,321 nonredundant proteins were successfully identified. Data were compared to predicted protein accessions for Ipomea species and mapped on the sweet potato transcriptome and haplotype-resolved genome. A proteogenomics analysis successfully mapped 12,902 peptides against the transcriptome or genome, representing 90.4% of the total 14,275 uniquely identified peptides, predicted 741 new protein-coding genes, and specified 2726 loci where annotations can be further improved. Overall, 39,916 peptides mapped to 3,143 unique proteins in leaves, and 34,339 peptides mapped to 2,928 unique proteins in roots; 32% and 27% unique identified proteins were leaves- and roots-specific, respectively.
2019-05-30 | PXD012999 | Pride
Project description:To screen genes related to the development of sweet potato tuberous roots, the high throughput sequencing of different stages of sweet potato tuberous roots was performed. The fibrous roots (FR; roots at 20 dap), developing tuberous roots (DR; roots at 60 dap) and mature tuberous roots (MR; roots at 120 dap) of Ipomoea batatas (L.) Taizhong 6 and MBP3 overexpressed lines were used for transcriptome analysis. Totally, we identified 5488 differentially expressed genes between different stage tuberous roots of Taizhong6 and 14312 differentially expressed genes between the tuberous roots of Taizhong6 and MBP3 overexpressed lines, by calculating the gene FPKM in each sample and conducting differential gene analysis. This study provides a foundation for the mechanism analysis of sweet potato tuberous root development.
2023-10-12 | GSE245185 | GEO
Project description:we performed de novo transcriptome assembly and digital gene expression (DGE) profiling analyses of sweet potato challenged with Fob using Illumina Hiseq technology. A total of 89,944,188 clean reads were generated and were assembled into 101,988 unigenes with an average length of 666bp, 62,605(61.38%) of them were functional annotated in the non-redundant(nr) protein database from NCBI by using BLASTX with a cut-off E-value of 10-5, and COG,GO and KEGG annotations were examined for better understand their functions. Five DGE libraries were constructed from the sweet potato cultivar JS57 (high resistance) and XZH (high susceptible) challenged with pathogenic and Nonpathogenic Fob. The differentially expressed genes including up- and down-regulation in five libraries were identified and calculated based on comparisons of transcriptomes, showing differences in gene expression profiles among the samples. A set of differentially expressed genes involved disease response were identified, including 40 WRKY and seven NAC transcription factors, four resistance genes, 22 pathogenesis-related genes, and six genes involved in SA signal pathway. Our study is the first to provide the transcriptome sequence resource of sweet potato challenged with pathogenic and non-pathogenic Fob and demonstrate its digital expression profiling. We discovered a set of genes involved in disease resistance. These data provides comprehensive sequence resource of sweet potato for genetic and genomic studies and will accelerate the understanding of molecular mechanism of disease resistance.
2018-02-13 | GSE89290 | GEO
Project description:Sweet potato virus disease (SPVD) is one of the most devastating diseases affecting sweetpotato (Ipomoea batatas), an important food crop in developing countries. SPVD develops when sweetpotato plants are dually infected with sweet potato feathery mottle virus (SPFMV) and sweet potato chlorotic stunt virus (SPCSV). In the current study, global gene expression between SPVD affected plants and virus-tested control plants (VT) were compared in the susceptible ‘Beauregard’ and resistant ‘NASPOT 1’ (Nas) sweetpotato cultivars at 5, 9, 13 and 17 days post inoculation (DPI).
2010-01-29 | GSE18869 | GEO
Project description:Citrus Huanglongbing (HLB, or greening) is one of the most severe diseases of citrus. Plant disease symptom development is considered to be the consequence of a number of molecular, cellular and physiological changes, and may also be associated with host defense responses. Understanding citrus host response to HLB may contribute to the development of new strategies to control this destructive disease. We performed microarray analysis to identify the differentially expressed genes in sweet orange in response to HLB infection using the Affymetrix GeneChipM-BM-. citrus genome array. Two-year-old seedlings of M-bM-^@M-^XMadam VinousM-bM-^@M-^Y sweet orange (Citrus sinensis L. Osbeck) were inoculated by grafting with bud sticks from HLB-diseased, PCR positive sweet orange plants. For mock-inoculated controls, the same types of plants were grafted with bud sticks from HLB-free, PCR negative sweet orange. At 7 months after inoculation, mature leaves were sampled from 3 individual HLB-diseased plants, and healthy leaves from 3 mock-inoculated plants as control. Total RNA was extracted from leaf samples and hybridized on Affymetrix microarrays.
2011-07-06 | E-GEOD-29633 | biostudies-arrayexpress
Project description:The formation and development of storage roots is an intricate process regulated via a complex transcriptional regulatory network. To significantly advance our understanding of the molecular mechanisms governing storage root initiation and development in sweet potato, we performed a comprehensive analysis of transcriptome dynamics during root development.
2021-10-31 | GSE172378 | GEO
Project description:HLB is suggested to be caused by the phloem-limited fastidious prokaryotic α-proteobacterium “Candidatus Liberibacter spp.” Previous studies focused on the proteome and transcriptome analyses of citrus 5 to 35-week-after “Ca. L. spp.” inoculation. In this study, gene expression profiles was analyzed using mandarin of Citrus reticulate Blanco cv. jiaogan leaves after 2-year infection with “Ca. L. asiaticus”. The Affymetrix GeneChip® citrus genome were applied to study the molecular pathways mediated by “Ca. L. asiaticus” inoculated 3-year-old jiaogan seedlings. Each of them was graft-inoculated with one sweet orange scions with or without “Ca. L. asiaticus” in Dectember, 2009. RNA samples from three mandarin trees infected with 'Candidatus Liberibacter asiaticus' and three uninfected trees were used for affymatrix genochip
2015-04-10 | E-GEOD-67376 | biostudies-arrayexpress