Ontology highlight
ABSTRACT:
PROVIDER: PRJNA628577 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11613500_1.fastq.gz | Fastqsanger.gz | |||
| SRR11613500_2.fastq.gz | Fastqsanger.gz | |||
| SRR11613501_1.fastq.gz | Fastqsanger.gz | |||
| SRR11613501_2.fastq.gz | Fastqsanger.gz | |||
| SRR11613502_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE4968: Sugarcane transcriptome - ABA treatment GSE4971: Sugarcane transcriptome - Drought response GSE14730: Expression profile in internodes 1, 5 and 9 from high and low brix plants for sucrose content GSE14731: Expression profile between internodes 1 and 9 from high and low brix plants for sucrose content Refer to individual Series
2010-06-30 | E-GEOD-14732 | biostudies-arrayexpress
Project description:Sugarcane (Saccharum hybrid, SP80-3280) was grown in the field in Araras (Brazil) for 9 months. Leaves +1 (F1), internodes 1&2 (I1), and internodes 5 (I5) were harvested every 2 h for 26 h, starting 2h before dawn.
2019-04-10 | GSE129543 | GEO
Project description:We performed cell wall proteins (CWPs) extraction and analysis from sugarcane 7-month-old young and mature leaves and basal and apical internodes in order to point the differences regarding the cell wall proteome composition in these specific organs and diverse developmental stages. We used two different extraction methods for leaves CWPs: destructive and non-destructive. For internodes, only the non-destructive technique was used. The collection of CWPs was identified through LC-MS/MS analyses. Altogether, 110 sugarcane CWPs were identified and classified into eight functional categories. Sugarcane has one of the highest coverage of CWPs identified by mass spectrometry, reaching 283.
2019-04-24 | PXD012761 | Pride
Project description:Summary The expression profile of internodes from high brix plant was compared to internodes from low brix plants. Mature (In9), intermediate (In5) and immature internodes (In1) were collected from two different Progenies and immediately frozen in liquid nitrogen. Total RNA was extracted using Trizol. Progeny 1 was derived from two intra-specific polycrosses, one among Saccharum officinarum genotypes and the other combining Saccharum spontaneum genotypes. For each generation, 500 individuals were sampled for brix content and gene expression. The extreme segregants were selected for further analysis. The F3 hybrid individuals selected for molecular studies were planted in a field in single rows of 5 m using standard sugarcane cultivation practices. Brix readings and tissue samples were collected very early in the season, and in March of the following year, when plants were 10 months old. The soluble solids (brix) content of mature internodes of each sugarcane stalk was measured with a portable refractometer (N1 model, ATAGO, Japan). Individuals or pools of eight individuals had their tissues collected and RNA extracted. Progeny 2 was derived from a cross between two commercial varieties (SP80-180 x SP80-4966). Five hundred sugarcane F1 plants were field-grown. The stem sugar content from the different plants showed a normal distribution, and seven plants with extreme brix values were collected. Keywords: Expression profiling by array
2009-02-12 | GSE14730 | GEO
Project description:Summary The expression profile of internodes from high brix plant was compared to internodes from low brix plants. Mature (In9), intermediate (In5) and immature internodes (In1) were collected from two different Progenies and immediately frozen in liquid nitrogen. Total RNA was extracted using Trizol. Progeny 1 was derived from two intra-specific polycrosses, one among Saccharum officinarum genotypes and the other combining Saccharum spontaneum genotypes. For each generation, 500 individuals were sampled for brix content and gene expression. The extreme segregants were selected for further analysis. The F3 hybrid individuals selected for molecular studies were planted in a field in single rows of 5 m using standard sugarcane cultivation practices. Brix readings and tissue samples were collected very early in the season, and in March of the following year, when plants were 10 months old. The soluble solids (brix) content of mature internodes of each sugarcane stalk was measured with a portable refractometer (N1 model, ATAGO, Japan). Individuals or pools of eight individuals had their tissues collected and RNA extracted. Progeny 2 was derived from a cross between two commercial varieties (SP80-180 x SP80-4966). Five hundred sugarcane F1 plants were field-grown. The stem sugar content from the different plants showed a normal distribution, and seven plants with extreme brix values were collected. Keywords: Expression profiling by array Total RNA from internodes pool from high brix plants and low brix plants was hybridized to dual channel arrays. Internodes from the same stage of development and from the same progeny were compared. The quantification of each hybridization was submitted in two files, one for each slide side (technical replicates).
2009-02-11 | E-GEOD-14730 | biostudies-arrayexpress
Project description:The expression profile of mature internodes (In9) and immature (In1) internodes of high brix and low brix plants was compared. Internodes were collected from plants with high brix content and from plants with low brix content from Progeny 2. Progeny 2 was derived from a cross between two commercial varieties (SP80-180 x SP80-4966). Five hundred sugarcane F1 plants were field-grown. The stem sugar content from the different plants showed a normal distribution, and seven plants with extreme brix values were collected 7 and 11 months after planting. Keywords: Expression profiling by array
2009-02-12 | GSE14731 | GEO
Project description:By characterizing the cell wall proteomes of different sugarcane organs (leaves and stems) at two developmental stages (young vs mature/apical vs basal), it was possible to address unique characteristics in each of them. Four-month-old leaves showed a higher proportion of oxido-reductases and proteins related to lipid metabolism (LM), besides a lower proportion of proteins acting on polysaccharides, in comparison to four-month-old internodes. It was possible to note that sugarcane leaves and young stems have the highest LM rate than all species, which was assumed to be linked to cuticle formation. The data generated enriched the number of cell wall proteins (CWPs) identified in sugarcane, reaching 277. To our knowledge, sugarcane has now the second higher coverage of monocot CWP in plants
2018-01-05 | PXD007893 | Pride
Project description:Sugarcane is an important crop in tropical regions of the world, producing a very large biomass and accumulating large amounts of sucrose in the stem. In this study, we present the first report of transcript profiling using the GeneChip Sugarcane Genome Array. We have identified transcripts that are differentially expressed in the sugarcane stem during development by expression profiling using the array and total RNA derived from three disparate stem tissues (meristem, internodes 1-3; internode 8; internode 20) from four replicates of the sugarcane variety Q117 grown in the field. We have identified 119 transcripts that were highly differentially expressed with stem development and have characterised members of the cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families which displayed coordinated expression during stem development. In addition, we determined that many other transcripts involved in cell wall metabolism and lignification were also co-expressed with members of the CesA and Csl gene families, offering additional insights into the dynamics of primary and secondary cell wall synthesis in the developing sugarcane stem. Keywords: stem development profile
2006-11-19 | GSE5021 | GEO
Project description:Sugarcane is an economically important crop contributing to the world’s sugar and ethanol production with 80% and 40%, respectively. In recent years, the growing demands for sugar and ethanol production has prompted the necessity to increase sugarcane productivity through conventional breeding programs. However, sugarcane breeders have encountered several difficulties to raise productivity, mainly due to its complex genetics. Sugarcane has a polyploidy genome, with many varieties being aneuploidy. Today, the majority of the planted sugarcane cultivars are complex hybrids derived mainly from crosses between Saccharum officinarum and S. spontaneum. Therefore, proteomics can provide some insight into deciphering gene regulation and changes in carbon metabolism and sucrose accumulation in the culms at different stages of plant development. The aim of this work was to compare the quantitative changes of proteins in sugarcane culms, during plant growth and sucrose accumulation. Total proteins were isolated from both, juvenile and maturing internodes at three stages of plant development. Label free shotgun proteomics was used for protein profiling and quantification. The internodes 5 (I5) and 9 (I9) of 4, 7 and 10 month-old-plants (4M, 7M and 10M, respectively) were harvested and used for proteomic analyses. To mimic field conditions of sucrose accumulation during sugarcane maturation, we stopped watering 10M plants for 10 days. An average of 1130 proteins, unique and differentially expressed across all ages were identified and quantified. Proteins were categorized within 27 functional groups, related to biological process. The patterns of expression for some categories, such as cellular amino acids, metabolic processes, secondary metabolic processes and translation were down-regulated in the immature internode (I5-10M), while up-regulated in the mature I9-10M. We observed an increase in the abundance of several enzymes of the glycolytic pathway and isoforms of alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC), in the juvenile stages of development of I9. These changes in enzymes contents indicates that at the early stages of internode development, hypoxia is increasing the glycolytic and ethanolic fermentation pathways, in order to supply ATP for plant growth and NAD+ for mitochondrial respiration, which might be impaired by the low oxygen availability inside the culm.
2021-09-09 | PXD027410 | Pride
Project description:Sugarcane accumulates high concentrations of sucrose in the mature stalk, with numerous physiological processes in maturing stalk tissue both directly and indirectly involved. A considerable portion of carbohydrate metabolism is also devoted to cell wall synthesis and fibre production. Previously, we have identified differentially expressed transcripts correlated with sucrose accumulation and fibre production in various internodes of the sugarcane stalk. In this study, we have examined tissue-specific expression patterns to further explore gene pathways responsible for sucrose accumulation and fibre synthesis. We performed large-scale expression profiling of storage parenchyma, vascular bundles and rind dissected from a maturing stalk internode from field-grown commercial sugarcane harvested at 11 months of age. We identified 10 cellulose synthase subunit genes in sugarcane and examined significant differences in the expression of their corresponding transcripts and those of several sugar transporters between the different tissues. These were further correlated with differential expression patterns for transcripts of specific COBRA-like proteins and other proteins with acknowledged roles in cell wall metabolism. We found that the sugar transporters ShPST2a, ShPST2b and ShSUT4 were significantly up-regulated in storage parenchyma while ShSUT1 was up-regulated in vascular bundles. Two co-ordinately expressed groups of cell wall related transcripts were also identified. One group which is associated with primary cell wall synthesis (ShCesA1, ShCesA7, ShCesA9 and Shbk2l3) was up-regulated in parenchyma. The other group which is associated with secondary cell wall synthesis (ShCesA10, ShCesA11, ShCesA12 and Shbk-2) was up-regulated in rind. We also report an unexpected paucity in differential expression of cell wall-related genes in vascular bundles. Our results indicate that there is spatial separation for elevated expression of these important targets in both sucrose accumulation and cell wall synthesis, allowing for increased clarity in our understanding of sucrose transport and fibre synthesis in sugarcane.
2015-10-13 | GSE67897 | GEO