Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15112700_1.fastq.gz | Fastqsanger.gz | |||
| SRR15112700_2.fastq.gz | Fastqsanger.gz | |||
| SRR15112701_1.fastq.gz | Fastqsanger.gz | |||
| SRR15112701_2.fastq.gz | Fastqsanger.gz | |||
| SRR15112702_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:MicroRNAs (miRNAs) are a class of endogenous non-coding small RNAs that regulate targeted mRNAs by degrading or repressing translation, considered as post-transcrption regulators. So far, a large number of miRNAs have been discovered in model plants, but little information is available on miRNAs in banana. In this study, by sequencing the small RNA (sRNA) transcriptomes of Fusarium wilt resistant and susceptible banana varieties, 139 members in 38 miRNA families were discovered, and six out of eight new miRNAs were confirmed by RT-PCR. According to the analysis of sRNA transcriptome data and qRT-PCR verification, some miRNAs were differentially expressed between Fusarium wilt resistant and susceptible banana varieties. Two hundred and ninety-nine and 31 target genes were predicted based on the draft maps of banana B genome and Fusarium oxysporum (FOC1, FOC4) genomes respectively. Specifically, two important pathogenic genes in Fusarium oxysporum genomes, feruloyl esterase gene and proline iminopeptidase gene, were targeted by banana miRNAs. These novel findings may provide a new strategy for the prevention and control of Fusarium wilt in banana.
2016-10-14 | GSE74005 | GEO
Project description:Background: Banana (Musa) is one of the most important crops grown in tropical and sub-tropical areas. Cavendish, the most widely grown banana cultivar, is a triploid derived from an intra-species cross. Cavendish is relatively resistant to Race 1 of Fusarium oxysporum f. sp. Cubense (Foc1) which caused wide spread Panama disease during 1960s but is susceptible to Race 4 of Foc (Foc4) which has been causing epidemics in large areas of banana fields in Asia and Australia in the last decade and is threatening world banana production. The genome of the diploid species Musa acuminata (AA) which is the ancestor of a majority of cultivated banana has recently been sequenced. Availability of banana transcriptomes will be highly useful for improving banana genome annotation and assembly and for banana biological research. The knowledge of global gene expression patterns influenced by infection by different Foc races will help to understand the pathogenesis processes and the host responses to the infection. Results: RNA samples extracted from different organs of the Cavendish cultivar were pooled for deep sequencing using the Illumina sequencing technology. The assembled reads were aligned with the genome of M. accuminata and with sequences in the Genbank databases. The analysis led to identification of 842 genes that were not annotated by the Musa genome project. A large number of simple nucleotide polymorphisms (SNPs) and short insertions and deletion (indels) were identified from the transcriptome data. GFP-expressing Foc1 and Foc4 was generated and used to monitor the infection process. Digital gene expression (DGE) profiling analysis was carried out to obtain transcriptome profiles influenced by infection with Foc1 and Foc4 in banana roots at 3, 27, and 51 hours post-inoculation. Both Foc1 and Foc4 were found to be able to invade banana roots and spread to root vascular tissues in the first two days following inoculation. The profiling analysis revealed that inoculation with Foc1 and Foc4 caused similar changes in the gene expression profiles in the infected banana roots. The Foc infection led to induction of many well-known defense-related genes including PATHOGENESIS-RELATED 5 (PR5), PAL, and a lignin-forming peroxidase. The WRKY40 gene, which is a negative regulator of the defense pathway in Arabidopsis, was quickly and strongly suppressed by the infection. Two genes encoding the ethylene biosynthetic enzyme ACC oxidase and several ethylene-responsive transcription factors were among strongly induced genes by both Foc1 and Foc4 Conclusions: Both Foc1 and Foc4 are able to spread into the vascular system of banana roots during the first two days of the infection process and their infection led to similar gene expression profiles in banana roots. The transcriptome profiling analysis indicates that the ethylene synthetic and signalling pathways were activated in response to the Foc infection. Digital gene expression (DGE) profiling analysis was carried out to obtain transcriptome profiles influenced by infection with Foc1 and Foc4 in banana roots at 3, 27, and 51 hours post-inoculation. The plants whose roots were immersed in the culture medium without the pathogen (mock inoculation) were used as a control.
2013-09-01 | E-GEOD-48563 | biostudies-arrayexpress
Project description:Background: Banana (Musa) is one of the most important crops grown in tropical and sub-tropical areas. Cavendish, the most widely grown banana cultivar, is a triploid derived from an intra-species cross. Cavendish is relatively resistant to Race 1 of Fusarium oxysporum f. sp. Cubense (Foc1) which caused wide spread Panama disease during 1960s but is susceptible to Race 4 of Foc (Foc4) which has been causing epidemics in large areas of banana fields in Asia and Australia in the last decade and is threatening world banana production. The genome of the diploid species Musa acuminata (AA) which is the ancestor of a majority of cultivated banana has recently been sequenced. Availability of banana transcriptomes will be highly useful for improving banana genome annotation and assembly and for banana biological research. The knowledge of global gene expression patterns influenced by infection by different Foc races will help to understand the pathogenesis processes and the host responses to the infection. Results: RNA samples extracted from different organs of the Cavendish cultivar were pooled for deep sequencing using the Illumina sequencing technology. The assembled reads were aligned with the genome of M. accuminata and with sequences in the Genbank databases. The analysis led to identification of 842 genes that were not annotated by the Musa genome project. A large number of simple nucleotide polymorphisms (SNPs) and short insertions and deletion (indels) were identified from the transcriptome data. GFP-expressing Foc1 and Foc4 was generated and used to monitor the infection process. Digital gene expression (DGE) profiling analysis was carried out to obtain transcriptome profiles influenced by infection with Foc1 and Foc4 in banana roots at 3, 27, and 51 hours post-inoculation. Both Foc1 and Foc4 were found to be able to invade banana roots and spread to root vascular tissues in the first two days following inoculation. The profiling analysis revealed that inoculation with Foc1 and Foc4 caused similar changes in the gene expression profiles in the infected banana roots. The Foc infection led to induction of many well-known defense-related genes including PATHOGENESIS-RELATED 5 (PR5), PAL, and a lignin-forming peroxidase. The WRKY40 gene, which is a negative regulator of the defense pathway in Arabidopsis, was quickly and strongly suppressed by the infection. Two genes encoding the ethylene biosynthetic enzyme ACC oxidase and several ethylene-responsive transcription factors were among strongly induced genes by both Foc1 and Foc4 Conclusions: Both Foc1 and Foc4 are able to spread into the vascular system of banana roots during the first two days of the infection process and their infection led to similar gene expression profiles in banana roots. The transcriptome profiling analysis indicates that the ethylene synthetic and signalling pathways were activated in response to the Foc infection.
2013-09-01 | GSE48563 | GEO
Project description:We report the high-throughput profiling of miRNAs in banana. By deep sequencing and computational and molecular analyses, we identify 113 known and 26 banana-specific miRNAs and we characterize their expression pattern under cold and heat stress. We find that 42 banana miRNAs are temperature-responsive. By degradome sequencing, we identify 60 targets for known miRNAs and half of these targets are regulated by 15 temperature-responsive miRNAs. The correlative expression patterns between several miRNAs and their target genes are further validated via qRT-PCR. Our results provide a foundation for understanding the miRNA-dependent temperature stress response in banana and the characterized correlations between miRNAs and their responses to cold or heat stress could serve as markers in the breeding programs or tools for biotechnological approaches for improving temperature stress tolerance of banana.
2018-09-18 | GSE77590 | GEO
Project description:We report the first data of RNA sequencing from two different banana cultivars from Musa acuminata cv. Mas Kirana (AA group) genome and Musa balbisiana cv. Klutuk (BB group) genome in response to blood disease infection caused by Ralstonia syzygii subsp. celebesensis (Rsc)
2019-11-18 | GSE138749 | GEO
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Small RNAs comprise a group of non coding RNAs which play significant role in the genetic regulation of growth and development in plants. The most important members of this family are the small inhibiting RNAs (siRNAs) and microRNAs (miRNAs). They are processed by the DICER like proteins in plants and incorporated into the RNA induced silencing complex to silence the cognate mRNAs by sequence specific cleavage. High throughput sequencing strategies have enabled the identification of complete gamut of small RNA sequences present in a plant tissue at a particular point of time enabling the study of their biological significance in different plant tissues. The small RNA profile of each plant shows few plant conserved sequences, few species specific sequences and few novel RNA sequences characteristic of each cultivar. Here we have performed high throughput sequencing of small RNA population derived from leaves of an elite edible Indian cultivar of banana cv. Rasthali (‘Silk’ subgroup with AAB genotype) to identify the microRNAs and other important small RNAs being expressed in the leaves of banana cv Rasthali. Generation of complete small RNA profile of banana cv. Rasthali for comparison with similar databases
2015-02-07 | E-GEOD-65728 | biostudies-arrayexpress
Project description:Small RNAs especially small inhibiting RNAs (siRNAs) and microRNAs (miRNAs) play essential role in the regulation of gene expression in plants. These non coding RNAs are processed by the DICER like proteins into 21-24 nucleotides single stranded molecules that guide the activity of RNA induced silencing complex. This complex along with the processed small RNA identifies the cognate mRNA and brings about sequence specific mRNA degradation thereby silencing the gene expression. The small RNA profile is unique for each plant tissue at a given point of time. High throughput sequencing method allows the study of differential expression of these small RNAs. Deep sequencing of small RNAs derived from the leaves of an elite cultivar of banana cv. Grand Naine (‘Cavendish’ subgroup with AAA genotype) was carried out. Generation of complete small RNA profile of banana cv. Grand Naine for comparison with similar databases
2015-02-07 | E-GEOD-65727 | biostudies-arrayexpress
Project description:Passiflora mollissima commonly known as “banana passion fruit” is usually consumed as fresh food or processed products, being seeds and peel the main by-products of the industrial processing. The potentially bioactive metabolites from banana passion fruit PLE-extract seeds have been recently characterized by HPLC-HRMS after sequential pressurized liquid extraction (PLE) To apply a Foodomics approach to study the effects of a banana passion fruit seeds PLE-extract (with high antioxidant capacity and enriched in phenolic-type compounds) on the transcriptome and metabolome of HT-29 colon cancer cells.
2022-05-24 | GSE133686 | GEO
Project description:Small RNAs comprise a group of non coding RNAs which play significant role in the genetic regulation of growth and development in plants. The most important members of this family are the small inhibiting RNAs (siRNAs) and microRNAs (miRNAs). They are processed by the DICER like proteins in plants and incorporated into the RNA induced silencing complex to silence the cognate mRNAs by sequence specific cleavage. High throughput sequencing strategies have enabled the identification of complete gamut of small RNA sequences present in a plant tissue at a particular point of time enabling the study of their biological significance in different plant tissues. The small RNA profile of each plant shows few plant conserved sequences, few species specific sequences and few novel RNA sequences characteristic of each cultivar. Here we have performed high throughput sequencing of small RNA population derived from leaves of an elite edible Indian cultivar of banana cv. Rasthali (‘Silk’ subgroup with AAB genotype) to identify the microRNAs and other important small RNAs being expressed in the leaves of banana cv Rasthali.
2015-02-07 | GSE65728 | GEO