Similar Datasets
Project description:A single-cell transcriptomic atlas of A. thaliana seed germination
| PRJNA755880 | ENA
Project description:This series analyses germinating Arabidopsis seeds with both temporal and spatial detail, revealing two transcriptional phases that are separated with respect to testa rupture. Performed as part of the ERA-NET Plant Genomics grant vSEED.
2013-07-16 | GSE41212 | GEO
Project description:This series analyses germinating Arabidopsis seeds with both temporal and spatial detail, revealing two transcriptional phases that are separated with respect to testa rupture. Performed as part of the ERA-NET Plant Genomics grant vSEED. Arabidopsis seeds were dissected into four tissues at nine time-points during seed germination. The tissues were the combined micropylar and chalazal endosperm (MCE), the remaining endosperm (PE), the radicle and embryonic axis (RAD) and the cotyledons (COT). At testa and endosperm rupture the seeds were sampled in separate pre- and post-ruptured populations.
2013-07-16 | E-GEOD-41212 | biostudies-arrayexpress
Project description:Extensive studies of the model plant Arabidopsis has enabled a deep understanding of organs and tissues throughout plant development. Yet, a fundamental understanding of cell types and states across organs and development is still lacking. Here, we present a single-nucleus transcriptome atlas of Arabidopsis seed-to-seed development encompassing diverse tissues across ten developmental time points. Analysis of over 400,000 nuclei revealed 183 major and 653 subclusters that demarcate cell type and state. Cross-organ analyses revealed that the transcriptional identity of many cell types is conserved across development but influenced by the organ of origin and developmental timing. In addition, groups of transcription factors were enriched and uniquely expressed in individual organs and time points, suggesting developmental gatekeeping of transcription factor activation. Finally, we employed spatial transcriptomics to validate our findings in the highly complex silique organ.
2023-03-25 | GSE226097 | GEO
Project description:This series analyses germinating Lepidium sativum seeds with both temporal and spatial detail. This is a cross species microarray normalisation on Arabidopsis thaliana chips. Performed as part of the vSEED project
2015-02-20 | GSE55702 | GEO
Project description:affy_rice_2011_03 - affy_compartimentation_rice_albumen_embryon - During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination. -We germinate rice seeds of the first sequenced rice cultivar i.e. Nipponbare during 0, 4, 8, 12, 16 and 24h of imbibition in sterile distilled water. Germination occurs under constant air bubbling, in the dark at 30°C. These rice seeds are then manually dissected into embryo and endosperm fractions. -The embryo-derived samples are abbreviated in “E” while the endosperm samples are abbreviated “A”. The germination time-point is indicated after the letter (e.g. E8 for embryo samples harvested after 8 hours of germination). Finally, the biological repetition number is indicated before the letter and the time digit (e.g. 1-E8 for an embryo sample from the first repetition at 8 hours of imbibition).
2013-07-01 | GSE43780 | GEO
Project description:affy_rice_2011_03 - affy_compartimentation_rice_albumen_embryon - During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination. -We germinate rice seeds of the first sequenced rice cultivar i.e. Nipponbare during 0, 4, 8, 12, 16 and 24h of imbibition in sterile distilled water. Germination occurs under constant air bubbling, in the dark at 30M-BM-0C. These rice seeds are then manually dissected into embryo and endosperm fractions. -The embryo-derived samples are abbreviated in M-bM-^@M-^\EM-bM-^@M-^] while the endosperm samples are abbreviated M-bM-^@M-^\AM-bM-^@M-^]. The germination time-point is indicated after the letter (e.g. E8 for embryo samples harvested after 8 hours of germination). Finally, the biological repetition number is indicated before the letter and the time digit (e.g. 1-E8 for an embryo sample from the first repetition at 8 hours of imbibition). 36 arrays - rice; organ comparison,time course
2013-07-01 | E-GEOD-43780 | biostudies-arrayexpress
Project description:12h Time-series transcriptome using VISUAL
| PRJDB19044 | ENA
Project description:Purpose: To identify the potential genes that regulate seed germination speed in maize, we performed a time-series transcriptome analysis with two inbred maize lines (72-3 fast germination, F9721 slow germination) during the seed germination and compared the differentially expressed genes (DEGs) in transcriptome with genes identified by GWAS Methods: Methods: mRNA profiles of two maize inbred lines 72-3 and F9721 showing divergent seed germination at six stages during germination were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed at the gene level. Hisat2 was used to align clean reads to maize B73 reference genome, and HTSeq was used to count transcript abundance. DESeq2 models were used to compare DEGs at each germination stage within or between samples Results: Comparative transcriptome study identified 12 hours after imbibition (HAI) as the critical stage responsible for the variation of germination speed. The DEGs between 72-3 and F9721 were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, oxidoreductase activity pathways, hormone signal transduction, and amino acid transporter activity pathways Conclusions: Combined with evidence from gene expression data, GWAS, and gene synteny with other model species, we finally anchored three genes as the likely candidate genes regulating germination speed in maize
2022-03-02 | GSE193292 | GEO
Project description: Not available
| S-EPMC9088103 | biostudies-literature