Ontology highlight
ABSTRACT:
PROVIDER: PRJNA904025 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22366948_1.fastq.gz | Fastqsanger.gz | |||
| SRR22366948_2.fastq.gz | Fastqsanger.gz | |||
| SRR22366949_1.fastq.gz | Fastqsanger.gz | |||
| SRR22366949_2.fastq.gz | Fastqsanger.gz | |||
| SRR22366950_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:affy_genomic_poplar - affy_genomic_poplar - The project aims to identify genes of interest for water deficit acclimation in poplar. We look for genes and gene expression networks related to drought stress in two hybrid cultivars, differing in their drought tolerance in field. Affymetrix poplar genome array was designed on several Populus species. In order to deal with comparative approaches, we checked the convenience of the array by hybridizing genomic DNA of the two hybrid cultivars (Populus deltoides × Populus nigra, namely ‘cv Carpaccio’ and ‘cv Soligo’). This point is important as transcript sequence might have diverged in the two genomes (Fossati et al, 2005), which could lead to absence of hybridization without physiological meaning. -Two poplar cultivars, Soligo (S) and Carpacio (C) were grown in controlled conditions. Mature leaves were collected and genomic DNA was extracted from leaves in CTAB buffer. gDNA was fragmented with DNAse1. DNA fragments were labelled with Biotin N6-ddATP and hybridized on Affymetrix poplar genome array. Two technical replicates per genotype were performed. Keywords: genomic comparison,gain of fuction epimutation
2011-04-01 | GSE21334 | GEO
Project description:affy_genomic_poplar - affy_genomic_poplar - The project aims to identify genes of interest for water deficit acclimation in poplar. We look for genes and gene expression networks related to drought stress in two hybrid cultivars, differing in their drought tolerance in field. Affymetrix poplar genome array was designed on several Populus species. In order to deal with comparative approaches, we checked the convenience of the array by hybridizing genomic DNA of the two hybrid cultivars (Populus deltoides × Populus nigra, namely ‘cv Carpaccio’ and ‘cv Soligo’). This point is important as transcript sequence might have diverged in the two genomes (Fossati et al, 2005), which could lead to absence of hybridization without physiological meaning. -Two poplar cultivars, Soligo (S) and Carpacio (C) were grown in controlled conditions. Mature leaves were collected and genomic DNA was extracted from leaves in CTAB buffer. gDNA was fragmented with DNAse1. DNA fragments were labelled with Biotin N6-ddATP and hybridized on Affymetrix poplar genome array. Two technical replicates per genotype were performed. Keywords: genomic comparison,gain of fuction epimutation 4 arrays - poplar
2011-04-01 | E-GEOD-21334 | biostudies-arrayexpress
Project description:Pentatricopeptide repeat (PPR) proteins, which are characterized by tandem 30-40 amino acid sequence motifs, constitute a large gene family in plants. These known PPR proteins have been identified to play important roles in organellar RNA metabolism and plant development in Arabidopsis and rice. However, functions of PPR genes in woody species remain still largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the poplar genome. A comprehensive genome-wide analysis of the poplar PPR gene family was performed, including chromosomal location, phylogenetic relationships, gene duplication. Transcriptomic analyses identified that 154 of the PtrPPR genes were induced by biotic and abiotic treatments, including Marssonina brunnea, salicylic acid (SA), methyl jasmonate (MeJA), wounding, cold and salinity. Quantitative RT-PCR analysis further confirmed the expression profiles of 11 PtrPPR genes under different stresses. Our results contribute to a more comprehensive understanding the roles of PPR proteins and provided an insight for improving the stress tolerance in poplar.
2018-01-31 | GSE109609 | GEO
Project description:Populus euphratica is a medium-sized deciduous tree naturally grown in high saline condition, however, the molecular response of the poplar to salinity at global genome level maintain to be elucidated. We used Affymetrix poplar genome microarrays to investigate the full transcript expression exposed to different salt intensities and identified significantly changed transcripts within the 24 hours after exposed to salt stress.
2016-11-12 | GSE52305 | GEO
Project description:Since metabolites are the net products of the central dogma of cellular biology, this study was aimed to decipher salinity tolerance depends on the information encoded by the metabolomic profiles of the salt tolerant ‘Umsila’ and susceptible ‘Zabad’ cultivars when grown under salinity. Changes in the metabolomic profiles of the leaf and root tissues were determined using hydrophilic interaction liquid chromatography (HILIC) and reverse phase liquid (RPLC) mass spectrometry.
2019-03-18 | ST001156 | MetabolomicsWorkbench
Project description:In the present study, we compared transcriptional response to salinity between male and female individuals of Populus yunnanensis. We found that several functional groups of genes involved in important pathways were differentially expressed, including photosynthesis-related genes which were mainly up-regulated in males but down-regulated in females. This gene expression pattern is consistent with physiological observation that salinity inhibited photosynthetic capacity more in females than in males. In conclusion, our study provided molecular evidence of sexual differences in poplar salinity tolerance. Identified sex-related genes in salinity tolerance and their functional groups will enhance our understanding of sexual differences to salinity stress at the transcription level.
2012-01-20 | GSE35223 | GEO
Project description:In the present study, we compared transcriptional response to salinity between male and female individuals of Populus yunnanensis. We found that several functional groups of genes involved in important pathways were differentially expressed, including photosynthesis-related genes which were mainly up-regulated in males but down-regulated in females. This gene expression pattern is consistent with physiological observation that salinity inhibited photosynthetic capacity more in females than in males. In conclusion, our study provided molecular evidence of sexual differences in poplar salinity tolerance. Identified sex-related genes in salinity tolerance and their functional groups will enhance our understanding of sexual differences to salinity stress at the transcription level. 4 samples examined: males without salinity stress, males exposed to salinity stress, females without salinity stress and females exposed to salinity stress. Nine plants of each sex were exposed to each treatment, and RNA samples from the 9 individuals were pooled with equal proportion.
2012-01-20 | E-GEOD-35223 | biostudies-arrayexpress
Project description:In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample. We collected seedlings of three rice cultivars subjected to control (kept in water), desiccation (transferred on folds of tissue paper) and salinity (transferred to beaker containing 200 mM NaCl solution) treatments. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to Japonica reference genome using Tophat software. Cufflinks was used for reference-based assembly and differential gene expression was studied using cuffdiff software. The differentially expressed genes during various abiotic stress conditions were identified.
2015-12-31 | E-GEOD-60287 | biostudies-arrayexpress