Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21928620_1.fastq.gz | Fastqsanger.gz | |||
| SRR21928620_2.fastq.gz | Fastqsanger.gz | |||
| SRR21928621_1.fastq.gz | Fastqsanger.gz | |||
| SRR21928621_2.fastq.gz | Fastqsanger.gz | |||
| SRR21928622_1.fastq.gz | Fastqsanger.gz |
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Project description:The long-lived sacred lotus (Nelumbo nucifera) fruit provides a good platform for uncovering aging-related mechanism in extension of seed-life and improving of food quality of economic crops during storage. Here, we investigated the proteome of artificial aging lotus seed to uncover the aging -resistance mechanism. Proteome was performed on the seeds embryo axis treated at 80C for 0, 12 and 24 Hours. We identified 4667 proteins, and found 383 and 37 proteins (folds>1.3, FDR<0.01) were differentially expressed from 0-12h and 12-24h treatment, respectively. This proteome data will provide a better understanding and give further insights on lotus seed aging-resistance.
2024-12-23 | PXD028436 | Pride
Project description:Unlike short interfering RNAs (siRNAs), which are commonly designed to repress a single messenger RNA (mRNA) target through perfect base pairing, microRNAs (miRNAs) are endogenous small RNAs that have evolved to concurrently repress multiple mRNA targets through imperfect complementarity. MicroRNA target recognition is primarily determined by pairing of the miRNA seed sequence (nucleotides 2–8) to complementary match sites in each mRNA target. Whereas siRNA technology is well established for single target knockdown, the design of artificial miRNAs for multi-target repression is largely unexplored. We designed and functionally analysed over 200 artificial miRNAs for simultaneous repression of pyruvate carboxylase and glutaminase by selecting all seed matches shared by their 3′ untranslated regions. Although we identified multiple miRNAs that repressed endogenous protein expression of both genes, seed-based artificial miRNA design was highly inefficient, as the majority of miRNAs with even perfect seed matches did not repress either target. Moreover, commonly used target prediction programs did not substantially discriminate effective artificial miRNAs from ineffective ones, indicating that current algorithms do not fully capture the features important for artificial miRNA targeting and are not yet sufficient for designing artificial miRNAs. Our analysis suggests that additional factors are strong determinants of the efficacy of miRNA-mediated target repression and remain to be discovered.
2014-02-28 | GSE50249 | GEO
Project description:Unlike short interfering RNAs (siRNAs), which are commonly designed to repress a single messenger RNA (mRNA) target through perfect base pairing, microRNAs (miRNAs) are endogenous small RNAs that have evolved to concurrently repress multiple mRNA targets through imperfect complementarity. MicroRNA target recognition is primarily determined by pairing of the miRNA seed sequence (nucleotides 2–8) to complementary match sites in each mRNA target. Whereas siRNA technology is well established for single target knockdown, the design of artificial miRNAs for multi-target repression is largely unexplored. We designed and functionally analysed over 200 artificial miRNAs for simultaneous repression of pyruvate carboxylase and glutaminase by selecting all seed matches shared by their 3′ untranslated regions. Although we identified multiple miRNAs that repressed endogenous protein expression of both genes, seed-based artificial miRNA design was highly inefficient, as the majority of miRNAs with even perfect seed matches did not repress either target. Moreover, commonly used target prediction programs did not substantially discriminate effective artificial miRNAs from ineffective ones, indicating that current algorithms do not fully capture the features important for artificial miRNA targeting and are not yet sufficient for designing artificial miRNAs. Our analysis suggests that additional factors are strong determinants of the efficacy of miRNA-mediated target repression and remain to be discovered. 293T cells were transiently transfected with artificial miRNAs or non-targeting control (Allstars siRNA, Qiagen). Three replicate transfections were performed for each miRNA or control. Total RNA was extracted 48 hours after transfection.
2014-02-28 | E-GEOD-50249 | biostudies-arrayexpress
Project description:Seed longevity is a crucial trait in agriculture as it determines the ability of seeds to maintain viability during dry storage. However, the molecular mechanism underlying seed aging and reduced seed longevity are currently not well understood. Here we report the comparative proteome and metabolome profiling of three rice cultivars varying in aging tolerance including an aging tolerant indica cultivar Dharial, an aging sensitive japonica cultivar Ilmi, and a moderately aging tolerant cultivar A2 that was generated by crossing between Dharial and Ilmi. Results obtained from comparative proteome and metabolome profiling suggest that aged seeds of all the cultivars utilize ubiquitin proteasome-mediated protein degradation which results in the accumulation of free amino acids in Ilmi while tolerant cultivars utilize those for energy production and synthesis of heat shock proteins, especially hsp20/alpha crystallin family protein. Additionally, aging tolerant cultivar seems to activate brassinosteroid signalling and suppress jasmonate signaling to initiate a signaling cascade that allows efficient detoxification of aging induced ROS to maintain the seed longevity during aging. Taken together, these results provide an in-depth understand of aging induced changes in rice seeds.
2024-01-10 | PXD043955 | Pride
Project description:Apple seeds were subjected to accelerated aging. After 7, 14, and 21 days of aging, embryos were isolated. Part of the embryos were shortly fumigated with nitric oxide (NO). After 48 h of embryos culture (aged embryos or aged embryos treated with NO), embryonic axes were used to extract the total RNA. RT-qPCR were done to analyze the changes in the expression of genes related to seed aging. Short-term (3 h) treatment of embryos isolated from accelerated aged apple seeds (Malus domestica Borkh.) with NO partially reduced the effects of aging. The aim of the study was to investigate the impact of the short-term NO treatment of embryos isolated from apple seeds subjected to accelerated aging on the expression of genes potentially linked to the regulation of seed aging. Apple seeds were artificially aged for 7, 14, or 21 days. Then the embryos were isolated from the seeds, treated with NO, and cultured for 48 h. Progression of seeds aging was associated with the decreased transcript levels of most of the analyzed genes (Lea1, Lea2a, Lea4, Hsp70b, Hsp20a, Hsp20b, ClpB1, ClpB4, Cpn60a, Cpn60b, Raptor, and Saur). The role of NO in the mitigation of seed aging depended on the duration of the aging. After 7 and 14 days of seed aging, a decreased expression of genes potentially associated with the promotion of aging (Tor, Raptor, Saur) was noted. NO-dependent regulation of seed aging was associated with the stimulation of the expression of genes encoding chaperones and proteins involved in the repair of damaged proteins. After NO application, the greatest upregulation of ClpB, Pimt was noted in the embryos isolated from seeds subjected to 7-day long accelerated aging, Hsp70b, Hsp70c, Cpn in the embryos of seeds aged for 14 days, and Lea2a in the embryos of seeds after 21 days of aging.
2022-07-07 | GSE207591 | GEO
Project description:•Cutin and suberin are lipid polyesters deposited in specific apoplastic compartments. Their fundamental roles in plant biology include controlling the movement of gases, water and solutes, and conferring pathogen resistance. Both cutin and suberin have been shown to be present in the Arabidopsis seed coat where they regulate seed dormancy and longevity. •In this study, we use accelerated and natural aging seed assays, glutathione redox potential measures, optical and transmission electron microscopy and gas chromatography-mass spectrometry to demonstrate that increasing the accumulation of lipid polyesters in the seed coat is the mechanism by which the AtHB25 transcription factor regulates seed permeability and longevity. •Chromatin immunoprecipitation during seed maturation revealed that the lipid polyester biosynthetic gene LACS2 (long-chain acyl-CoA synthetase 2) is a direct AtHB25 binding target. Gene transfer of this transcription factor to wheat and tomato demonstrates the importance of apoplastic lipid polyesters for the maintenance of seed viability. •Our work establishes AtHB25 as a trans-species regulator of seed longevity and has identified the deposition of apoplastic lipid barriers as a key parameter to improve seed longevity in multiple plant species.
2021-03-31 | GSE154886 | GEO
Project description:Proteomics raw data for “Acer truncatum seed oil alleviates learning and memory impairments of aging mice”
2021-03-16 | PXD024948 |