Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1131926 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29708300_1.fastq.gz | Fastqsanger.gz | |||
| SRR29708300_2.fastq.gz | Fastqsanger.gz | |||
| SRR29708301_1.fastq.gz | Fastqsanger.gz | |||
| SRR29708301_2.fastq.gz | Fastqsanger.gz | |||
| SRR29708302_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Background: Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during fruit ripening and its control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana. Results: Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes and some of them had their expression validated by qPCR. The transcription profile was then compared with that from ripening tomato and grape. Overall, the transcriptomics analysis revealed many similarities between ripening in papaya and tomato especially with respect to primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicate that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families are involved in the control of papaya ripening and reveal that cell wall-related gene expression in papaya showed similarities to the expression profiles seen in A. thaliana during hypocotyl development. Conclusion: The cross-species array experiment was successful in identifying ripening-related genes in papaya. The data indicated common and diverse elements of transcription control between fruit bearing taxa and has also indicated a possible distinct co-evolutionary mechanism for papaya cell wall disassembling system. The present study represents new topics for future researches that would help complement the structural genomic data provided by the papaya genome, since there is no gene-chip available for this plant organism. Papaya ripe transcriptome was analysed using mRNA extracted from unripe and ripe fruit from 2 replicates. After microarray hybridization in ATH1-121501 chip, data were normalized against data generated by papaya DNA hybridization in another ATH1-121501 chip and analysed using perl algorithms (masks).
2012-05-24 | E-GEOD-38105 | biostudies-arrayexpress
Project description:Background: Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during fruit ripening and its control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana. Results: Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes and some of them had their expression validated by qPCR. The transcription profile was then compared with that from ripening tomato and grape. Overall, the transcriptomics analysis revealed many similarities between ripening in papaya and tomato especially with respect to primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicate that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families are involved in the control of papaya ripening and reveal that cell wall-related gene expression in papaya showed similarities to the expression profiles seen in A. thaliana during hypocotyl development. Conclusion: The cross-species array experiment was successful in identifying ripening-related genes in papaya. The data indicated common and diverse elements of transcription control between fruit bearing taxa and has also indicated a possible distinct co-evolutionary mechanism for papaya cell wall disassembling system. The present study represents new topics for future researches that would help complement the structural genomic data provided by the papaya genome, since there is no gene-chip available for this plant organism.
2012-05-25 | GSE38105 | GEO
Project description:For identifying genes for sex determination in papaya, digital gene expression analysis by Ht-SuperSAGE (Matsumura et al., 2010) was carried out in flowers from male, female and hermaphrodite plants of papaya. Total more than 9,273,744 26bp-tags were obtained by sequence analysis using SOLiD3 and mapped on papaya primitive sex chromosome sequences.
2012-07-16 | GSE30366 | GEO
Project description:For identifying genes for sex determination in papaya, digital gene expression analysis by Ht-SuperSAGE (Matsumura et al., 2010) was carried out in flowers from male, female and hermaphrodite plants of papaya. Total more than 9,273,744 26bp-tags were obtained by sequence analysis using SOLiD3 and mapped on papaya primitive sex chromosome sequences. 6 samples examined: male young flowerbud, male mature flower bud, female young flower bud, female mature flower bud, hermaphrodite young flower bud, hermaphrodite mature flower bud
2012-07-15 | E-GEOD-30366 | biostudies-arrayexpress
Project description:The freeze-thaw awakening is a method in which seeds or germ cells prior to germination are slowly cooled, stored, and thawed to promote growth. To further test the validity of this method, we applied freeze-thaw awakening treatment on papaya seeds. When the seed was grown under room temperature (15-25C), the germination rate increased by more than 40% compared to those that were not subjected to the method. At 60 days post germination, the plant’s height was about 1.4 times as high as that of the untreated control. In addition, when both samples were grown in the field for about a year and a half, the treated showed darker green leaf color and an increase of seedlings per seed compared to the control. No significant difference in weight per fruit was observed. Comprehensive gene expression analysis of papaya leaves using RNA-seq showed more than 1000 differentially expressed genes, of which had genes involved in plant hormone synthase and environmental stress response. From these results, we show here that freeze-thaw-awakening is an effective method in promoting papaya growth.
2019-04-24 | GSE130188 | GEO
Project description:The Babaco Mosaic Virus (BabMV) is a Potexvirus that affects babaco (Vasconcellea heilbornii) and papaya (Carica papaya) plants. To understand the impact of the virus on the plant, we performed a genome-wide transcriptome analysis of the response of young leaves of 3-4 months old papaya plants at 2, 10, 15- and 30-days post infection (dpi) in comparison to uninfected controls. Results showed that in mock-infected plants and virus-infected plants at 2 and 10dpi more than 90% of the reads mapped to the papaya genome. In contrast, at 15 and 30 dpi only 31% mapped to the papaya genome in BabMV infected leaves, while the remaining 69% of the reads aligned to the virus genome, demonstrating a high viral load. A total of 1585 papaya genes were differentially expressed between mock and BabMV inoculated leaves, among which cell wall biogenesis, redox signaling, and ribosome Gene Ontology terms were overrepresented, interestingly, the virus induced specific responses at different time points. Sugar metabolism and cell wall modification including lignin accumulation genes were affected at 15 dpi. At 30 days post-infection, the virus primarily induced ROS production, possibly through the activation of cytochrome P450 enzymes. This led to the upregulation of genes associated with ROS scavenging and of transcription factors (TFs) belonging to the WRKY and AP2/ERF families, which play crucial roles in activating the plant's defense mechanisms against viral pathogens. This research enhances our understanding of BabMV infections, facilitating the development of effective disease control measures.
2025-05-30 | GSE266643 | GEO
Project description:To uncover a suit of genes related to the consumer preferred flavours, whole RNA sequencing followed by de novo genome assembly was performed on extreme flavoured papaya varieties RB1 (preferred with sweet flavour and floral aroma) and 1B (non-preferred with bitter flavour and musty aroma) fruits at ripe and unripe stages. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different papaya varieties at ripe and unripe stages.
2022-09-19 | GSE213436 | GEO
Project description:LNCaP cells were cultures in steroid depleted medium for 5 days before treatment with synthetic androgen (R1881, 10nM) for 16h. Transcriptomics analysis was performed to compare gene expression changes induced by androgen withdrawal or androgen treatment.
2013-10-22 | GSE51460 | GEO
Project description:Objective: To explore the mechanism of Jiangtang Tiaozhi Recipe in the treatment of obese T2DM patients with dyslipidemia based on transcriptomics. Methods: We chose 6 patients with obese type 2 diabetes mellitus and dyslipidemia (syndrome of excess of gastrointestinal heat) who were treated by JTTZR for 24 weeks, while 6 cases included in the healthy control group. We selected 6 cases in each group (disease group before treatment, disease group after treatment and healthy control group) to start the research of lncRNA microarray. According to the differentially expressions of lncRNAs and mRNAs, we secondly performed GO analysis, Pathway analysis, and found out some target lncRNAs as well as their associated mRNAs. The trial register number is NCT04623567. Results: (1) Disease group before treatment vs. healthy control group: There are 557 upregulated lncRNAs, 273 downregulated lncRNAs, 491 upregulated mRNAs and 1639 downregulated mRNAs. (2) Disease group after treatment vs. Disease group before treatment: There are 128 upregulated lncRNAs, 32 downregulated lncRNAs, 45 upregulated mRNAs and 140 downregulated mRNAs.
2022-01-14 | GSE193626 | GEO
Project description:The aim of this research was to study the effects of cis-element differences between the X, Y and Yh alleles on the expression of CpMDAR4, a potential candidate gene for sex differentiation in papaya, using a transcriptional reporter system in a model species Arabidopsis thaliana. Possible effects of a retrotransposon insertion in the Y and Yh alleles on the transcription and expression of CpMDAR4 alleles in papaya flowers were also examined. When comparing promoters and cis-regulatory elements among genes in the non-recombining region of the sex chromosomes, paired genes exhibited differences. Our results showed that differences in the promoter sequences of the CpMDAR4 alleles drove the expression of a reporter gene to different flower tissues in Arabidopsis. β-glucuronidase staining analysis of T2 and T3 lines for constructs containing 5’ deletions of native Y and Yh allele promoters showed the loss of specific expression of the reporter gene in the anthers, confirming the existence and location of cis-regulatory element POLLEN1LELAT52. The expression analysis of CpMDAR4 alleles in papaya flowers also showed that all alleles are actively expressed in different flower tissues, with the existence of a shorter truncated isoform, with unknown function, for the Y and Yh alleles due to an LTR-RT insertion in the Y and Yh chromosomes. The observed expression patterns in Arabidopsis thaliana flowers and the expression patterns of CpMDAR4 alleles in papaya flowers, suggest that MDAR4 might have a role on development of reproductive organs in papaya, and that it constitutes an important candidate for sex differentiation.
2022-07-18 | GSE208265 | GEO