Transcriptome analysis of wild type and sweet1 seeds upon treatments during germination
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ABSTRACT:
PROVIDER: PRJNA684572 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13242424_1.fastq.gz | Fastqsanger.gz | |||
| SRR13242424_2.fastq.gz | Fastqsanger.gz | |||
| SRR13242425_1.fastq.gz | Fastqsanger.gz | |||
| SRR13242425_2.fastq.gz | Fastqsanger.gz | |||
| SRR13242426_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome analysis of sweet1 seeds upon treatments during germination
| PRJNA794834 | ENA
Project description:Purpose: The goals of this study are to compare the transcriptome profiling between wild type and sweet1 under the treatments of either the glucose, ABA or both during germination. Methods: After 3-day imbibition, WT and sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C for 24 hours. Seeds were transferred to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment. Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche). The libraries were sequenced by Hiseq 2500 (Illumina) with paired-end reads. Results: Gene expression level was quantified using Kallisto v 0.44.0 by mapping to Arabidopsis thaliana (version 11) primary transcript sequences. Samples were evaluated based on pair-wise comparison between different conditions and outliers within each treatment were removed for the further analysis based on PCA results. There are 6230 candidates with more than 10 counts per million reads in at least 50% samples, |b| ≥ 0.2 and q-value < 0.05 were identified as differentially expressed genes (DEGs) using Sleuth program. Hierarchical clustering of DEGs uncovered several pathways that may contribute to glucose antagonizing ABA function. Conclusions: This study represents the detailed analysis of transcriptome in germinating seeds under ABA+Glc treatment. Our study provides a new perspective on the interaction between ABA and Glc in response to external stimuli to control the seed germination.
2021-06-30 | GSE163057 | GEO
Project description:Purpose: The goals of this study are to compare the transcriptome profiling between wild type and sweet1 under the treatments of either the glucose, ABA or both during germination. Methods: After 3-day imbibition, sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C for 24 hours. Seeds were transferred to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment. Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche). The libraries were sequenced by Hiseq 2500 (Illumina) with paired-end reads. Results: Gene expression level was quantified using Kallisto v 0.44.0 by mapping to Arabidopsis thaliana (version 11) primary transcript sequences. Samples were evaluated based on pair-wise comparison between different conditions and outliers within each treatment were removed for the further analysis based on PCA results. Candidates with more than 10 counts per million reads in at least 50% samples, |b| ≥ 0.2 and q-value < 0.05 were identified as differentially expressed genes (DEGs) using Sleuth program. Hierarchical clustering of DEGs uncovered several pathways that may contribute to glucose antagonizing ABA function. Conclusions: This study represents the detailed analysis of transcriptome in germinating seeds under ABA+Glc treatment. Our study provides a new perspective on the interaction between ABA and Glc in response to external stimuli to control the seed germination.
2023-01-01 | GSE193111 | GEO
Project description:Transcriptomic study of the impact of osmopriming on rape seeds (Brassica napus L.; cv 'Libomir') during priming process and after germination. The assays were replicated twice on two independent priming and germination experiments. Seeds were osmoprimed in PEG solution (-1.2 MPa osmotic potential) during 7 days, dried to initial moisture content and then germinated for 7 hours on water. The analysis during different phases of priming procedure (soaking and drying), after whole osmopriming process and germination were done.
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Project description:Transcriptomic study of the impact of osmopriming on rape seeds (Brassica napus L.; cv 'Libomir') during priming process and after germination. The assays were replicated twice on two independent priming and germination experiments. Seeds were osmoprimed in PEG solution (-1.2 MPa osmotic potential) during 7 days, dried to initial moisture content and then germinated for 7 hours on water. The analysis during different phases of priming procedure (soaking and drying), after whole osmopriming process and germination were done. 10 samples, four condition experiment; non dried primed seeds (Pnd) vs. dry unprimed seeds (UPd) (PEG soaking), non dried primed seeds (Pnd) vs dry primed seeds (Pd) (drying after soaking), dry primed seeds (Pd) vs. dry unprimed seeds (UPd) (full osmopriming process), primed seeds imbibed on water (P7h) vs unprimed seeds imbibed on water (UP7h) (germination after osmopriming). Biological replicates: 2 replicates for comparison PEG soaking, drying after soaking, full osmopriming process and germination after osmopriming.
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2017-02-01 | GSE93181 | GEO
Project description:Transcriptome changes were investigated for Euphorbia esula (leafy spurge) seeds with a focus on the effect of constant and diurnal fluctuating temperature on dormancy and germination. Leafy spurge seeds do not germinate when incubated for 21 days at 20°C constant temperatures, but nearly 30% germinate after 21 days under fluctuating temperatures 20:30°C (16:8 h). Incubation at 20°C for 21 followed by 20:30°C resulted in approximately 63% germination in about 10 days. A cDNA microarray representing approximately 22,000 unique sequences was used to profile transcriptome changes.
2010-06-01 | GSE18533 | GEO
Project description:In order to study the role of SlLBD40 and WRKY37 in seed germination, we established two gene knockout lines respectively. We then used RNA-seq data from seeds 6 h after imbibition of WT and two gene knockout lines for gene expression profiling.
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Project description:The mads-box mutant line showed an abscisic acid (ABA)-insensitive phenotype. The AGAMOUS-LIKE 67 (AT1G77950) gene encodes a transcription factor that is nuclear-localized, as observed by transiently transformed epidermal onion cells, specifically expressed in seeds and involved in an ABA signaling pathway during seed germination (Fernández-Arbaizar et al. 2012). SALK_050367 seeds were obtained from the Arabidopsis Biological Resource Center, ABRC.
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Project description:Transcriptional profiling of Arabidopsis far-red light pulse treated seeds comparing luh mutant with wild type (Col-0). Seeds were imbibed within 1 hr under white light and treated far-red light pulse for 5 min followed by 12 hr dark incubation. Goal was to determine the effects of LUH as transcriptional co-regulator during seed germination process.
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