A Spatial Transcriptome for Germinating Barley Grain
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA906477 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22443200_1.fastq.gz | Fastqsanger.gz | |||
| SRR22443200_2.fastq.gz | Fastqsanger.gz | |||
| SRR22443201_1.fastq.gz | Fastqsanger.gz | |||
| SRR22443201_2.fastq.gz | Fastqsanger.gz | |||
| SRR22443202_1.fastq.gz | Fastqsanger.gz |
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Project description:A spatial resolved transcriptome for germinating barley grain was obtained for over 14,000 genes at 0, 1, 3 6 and 24 hours after imbibition. The spatial expression of a number of genes was validated using in-situ PCR, quantitative comparison to bulk RNA-seq reveal good correlations, despite the differences in the methodologies, and marker gene definition for tissues/clusters was consistent with previous gene specific studies. Targeted analysis of genes encoding aquaporins, crucial for water and ion movement during germination, revealed specific spatial expression patterns for gene members, and the tissue specific changes in gene members over time. Highly restricted spatial (and temporal) expression patterns were observed for genes encoding cell wall and transcription factors, e.g. one of the strongest expressed transcription factors was a bZIP family member that responds to germinating promoting Karrikin. It’s expression was restricted to the scutellum and the adjacent endosperm (0-3 HAI) and declined afterwards. Discovery-based bio-informatic approaches revealed thousands of genes displayed a spatially restricted pattern within tissues, with gene ontology revealing enriched categories such as auxin related functions of transport and response factors displaying distinct spatial expression patterns in tissues. This provides unprecedented spatial resolved cellular map for germination and specific genes to target for functional genomics to define cellular restricted processes in tissues during germination.
2023-08-30 | GSE218970 | GEO
Project description:Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip. Experiment Overall Design: Barley developing and germinating seeds were harvested at different time points after flowering (developing) and imbibition (germinating). To further disseect the influence of different tissues, seeds were dissecte and tissues were analyzed individually.
2008-06-16 | E-GEOD-9365 | biostudies-arrayexpress
Project description:Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip. Keywords: time course
2007-12-20 | GSE9365 | GEO
Project description:Effect of high grain protein locus on barley grain protein accumulation. Gene expression levels were analysed in Karl, a low grain protein variety with its near-isogenic line 10_11(has high grain protein locus, chromosome 6)using Barley1 22k affymetrix chip. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Aravind Jukanti. The equivalent experiment is BB53 at PLEXdb.]
2011-11-22 | GSE33413 | GEO
Project description:Seed germination triggers a transition of growth and metabolic activities from quiescent to active statuses. Germinating seeds is a good system to study many biological and biochemical processes including hormone metabolic activities and cell wall biosynthesis. Next generation sequence technology is used to study these processes. We have examined gene transcription activities and alternative splicing events in germinating embryos We dissected barley embryos from four barley varieties at 2 time points 24 h and 48 h
2016-02-18 | E-GEOD-66024 | biostudies-arrayexpress
Project description:Effect of high grain protein locus on barley grain protein accumulation. Gene expression levels were analysed in Karl, a low grain protein variety with its near-isogenic line 10_11(has high grain protein locus, chromosome 6)using Barley1 22k affymetrix chip. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Aravind Jukanti. The equivalent experiment is BB53 at PLEXdb.] developmental stage: 14 days past anthesis - genotype: Karl - tissue type: Leaves(3-replications); developmental stage: 14 days past anthesis - genotype: Karl - tissue type: Kernels(3-replications); developmental stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves(3-replications); developmental stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels(3-replications); developmental stage: 21 days past anthesis - genotype: Karl - tissue type: Leaves(3-replications); developmental stage: 21 days past anthesis - genotype: Karl - tissue type: Kernels(3-replications); developmental stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves(3-replications); developmental stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels(3-replications)
2011-11-22 | E-GEOD-33413 | biostudies-arrayexpress
Project description:Proteomics can be used to assess individual protein abundances, which could reflect genotypic and/or environmental effects and potentially predict grain/malt quality. In this study, 79 barley grain samples from a Californian multi-environment trial were assessed using liquid chromatography-mass spectrometry. A total of 3105 proteins were identified across all samples. Location, genotype, and year explained 26.7%, 17.1%, and 14.3% of variance in the relative abundance of individual proteins, respectively. Sixteen proteins with storage, DNA/RNA binding, or enzymatic functions were found to be significantly higher/lower in abundance (compared to the overall mean) in the Yolo 3 and Imperial Valley locations, Butta 12 and LCS Odyssey genotypes, and 2017-18 and 2021-22 years. Individual protein abundances were reasonably predictive (RMSECV=1.25-2.04%) for total, alcohol-soluble, and malt protein content and malt fine extract. This study illustrates the role of the environment on the barley proteome and the utility of proteomics and machine learning to predict grain/malt quality.
2024-10-14 | MSV000096087 | MassIVE
Project description:Proteomic profiling was performed on barley spent grain. Spent grain from malted barley and from raw barley supplemented with exogenous enzymes were profiled.
2018-03-23 | PXD008090 | Pride
Project description:RNA-seq of germinating barley embryos in control and ABA
| PRJEB74509 | ENA
Project description:Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.
| S-EPMC10450182 | biostudies-literature