RNAseq of Brassica napus seed
Ontology highlight
ABSTRACT:
ORGANISM(S): Brassica napus
PROVIDER: GSE271809 | GEO | 2024/07/15
REPOSITORIES: GEO
Similar Datasets
Project description:Tissues were isolated from the globular seed using laser microdissection. At least two bioreplicates are included for each tissue. Tissues examined are : the embryo proper (EP), micropylar endosperm (MCE), peripheral endosperm (PEN), chalazal endosperm (CZE), chalazal proliferating tissue (CPT), chalazal seed coat (CZSC), inner seed coat (ISC), and outer seed coat (OSC).
2019-01-15 | GSE120360 | GEO
Project description:We collected globular stage seed compartments from 5 or 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of an Arabidopsis seed containing a globular stage embryo. For the purposes of this study we broke down the seed into 7 capturable compartments: embyro proper, suspensor, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and general seed coat. Experiment Overall Design: Globular stage seed compartments were isolated using the LMD6000 system. Total RNA was amplified and hybridized with Affymetrix ATH1 Arabidopsis array for 15 samples (Embryo Proper, Micropylar Endosperm, Peripheral Endosperm, General Seed Coat and Chalazal Seed Coat, 2 biological replicates each and Chalazal Endosperm with 3 biological replicates).
2008-06-11 | E-GEOD-11262 | biostudies-arrayexpress
Project description:We collected pre-globular stage seed compartments from 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of seeds containing pre-globular-stage embryos was identified as those seeds containing embryo propers made up of between 2 and 8 cells. For the purposes of this study we captured 6 compartments: embyro proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and general seed coat. Serial sections of entire seeds were also captured for comparison. Experiment Overall Design: Pre-globular stage seed compartments or whole seeds were isolated using the LMD6000 system. Total RNA was amplified and hybridized with Affymetrix ATH1 Arabidopsis array for 14 samples (embryo proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, general seed coat, chalazal seed coat, whole seeds, 2 biological replicates each).
2008-10-21 | E-GEOD-12402 | biostudies-arrayexpress
Project description:We collected globular stage seed compartments from 5 or 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of an Arabidopsis seed containing a globular stage embryo. For the purposes of this study we broke down the seed into 8 capturable compartments: embyro proper, suspensor, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat, general seed coat, and whole seeds. Keywords: cell type comparison
2008-04-25 | GSE11262 | GEO
Project description:We collected pre-globular stage seed compartments from 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of seeds containing pre-globular-stage embryos was identified as those seeds containing embryo propers made up of between 2 and 8 cells. For the purposes of this study we captured 6 compartments: embyro proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and general seed coat. Serial sections of entire seeds were also captured for comparison. Keywords: cell type comparison
2008-08-12 | GSE12402 | GEO
Project description:We profiled the gene regulatory landscape of Brassica napus reproductive development using RNA sequencing. Comparative analysis of this nascent allotetraploid across the plant lifecycle revealed the contribution of each subgenome to plant reproduction. Global mRNA profiling across reproductive development revealed lower accumulation of C subgenome transcripts relative to the A subgenome. Subgenome-specific transcriptional networks identified distinct transcription factor families enriched in each of the A and C subgenome in early seed development. Analysis of a tissue specific transcriptome of early seed development revealed transcription factors predicted to be regulators encoded by the A subgenome are expressed primarily in the seed coat whereas regulators encoded by the C subgenome were expressed primarily in the embryo. Whole genome transcription factor networks identified BZIP11 as an essential regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in knockdown of predicted target genes, and a reproductive-lethal phenotype. Our data indicate that subgenome bias are characteristic features of the B. napus seed throughout its development, and that such bias might not be universal across the embryo, endosperm, and seed coat of the developing seed. We also find that examining transcriptional networks spanning both the A and C genomes of the whole B. napus seed can identify valuable targets for seed development research. We suggest that-omics level approaches to studying gene regulation in B. napus can benefit from both broad and high-resolution analyses.
2021-08-31 | GSE144771 | GEO
Project description:High temperature stress results in yield loss and alterations to seed composition during seed filling in oilseed rape (Brassica napus). However, the mechanism underlying this heat response is poorly understood. In this study, we employed a microarray analysis with silique walls and seeds from the developing siliques (20 days after flowering) of Brassica napus that had undergone heat stress.
2015-01-05 | GSE57697 | GEO
Project description:We collected mature green seed compartments from 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing mature green-stage embryos. For the purposes of this study we captured 6 compartments: embryo proper, micropylar endosperm, cellularized peripherial endosperm, chalazal endosperm, chalazal seed coat and seed coat, as well sets of serial sections encompassing the entire mature green stage seed. Experiment Overall Design: Mature green stage seed compartments were isolated using the LMD6000 system. Total RNA was amplified and hybridized with Affymetrix ATH1 Arabidopsis array for 14 samples (embryo proper, micropylar endosperm, peripherial endosperm, chalazal endosperm, chalazal seed coat, seed coat and whole seeds, 2 biological replicates each).
2009-03-21 | E-GEOD-15165 | biostudies-arrayexpress
Project description:We collected heart stage seed compartments from 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing heart stage embryos. For the purposes of this study we captured 6 compartments: embryo proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and seed coat, as well sets of serial sections encompassing the entire heart stage seed. Experiment Overall Design: Heart stage seed compartments were isolated using the LMD6000 system. Total RNA was amplified and hybridized with Affymetrix ATH1 Arabidopsis array for 16 samples (embryo proper, micropylar endosperm, peripheral endosperm, seed coat and whole seeds, 2 biological replicates each; chalazal endosperm, chalazal seed coat, 3 biological replicates each).
2009-03-21 | E-GEOD-15160 | biostudies-arrayexpress
Project description:High temperature stress results in yield loss and alterations to seed composition during seed filling in oilseed rape (Brassica napus). However, the mechanism underlying this heat response is poorly understood. In this study, we employed a microarray analysis with silique walls and seeds from the developing siliques (20 days after flowering) of Brassica napus that had undergone heat stress. Two-condition experiment, control vs heat stress, 2 time points
2015-01-05 | E-GEOD-57697 | biostudies-arrayexpress