Comparative Transcriptomics Analysis of Red (Wild) and Orange (Modified) Carrots Available in India
Ontology highlight
ABSTRACT:
ORGANISM(S): Daucus carota subsp. sativus
PROVIDER: GSE179859 | GEO | 2021/12/31
REPOSITORIES: GEO
Similar Datasets
Project description:Comparative Transcriptomics Analysis of Red (Wild) and Orange (Modified) Carrots Available in India
| PRJNA745346 | ENA
Project description:In this study, a cross species hybridization (CSH) approach was used to evaluate whole transcriptome changes during carotenoid accumulation in the storage root of carrot (Daucus carota). Carotenoids are isoprenoid compounds providing red, yellow and orange color to plants. Previous gene expression analyses of carotenoid accumulation in non-model plant species have primarily used a candidate gene approach. Since global transcriptome analyses require extensive genome sequence, in the absence of these genomic resources an alternate approach uses platforms developed for model plant species. To assess transcriptome patterns associated with carotenoid pigmentation in carrot storage root, two carrot sibling inbred lines, B8788, true breeding for orange color and B8750, true breeding for white root color, were hybridized to the Medicago Affymetrix GeneChip microarray.
2014-08-13 | GSE49873 | GEO
Project description:In this study, a cross species hybridization (CSH) approach was used to evaluate whole transcriptome changes during carotenoid accumulation in the storage root of carrot (Daucus carota). Carotenoids are isoprenoid compounds providing red, yellow and orange color to plants. Previous gene expression analyses of carotenoid accumulation in non-model plant species have primarily used a candidate gene approach. Since global transcriptome analyses require extensive genome sequence, in the absence of these genomic resources an alternate approach uses platforms developed for model plant species. To assess transcriptome patterns associated with carotenoid pigmentation in carrot storage root, two carrot sibling inbred lines, B8788, true breeding for orange color and B8750, true breeding for white root color, were hybridized to the Medicago Affymetrix GeneChip microarray. Near isogenic recombinant inbred lines B8788 and B8750, derived from a cross between white rooted wild carrot (QAL) and orange-rooted B493 were used for comparative analyzes to minimize background genetic differences. B8788 is true breeding for orange color whereas B8750 is true breeding for white storage root color. Carrots were grown in three pots for each genotype under greenhouse conditions and carrots were selected arbitrarily from these pots for harvest. Roots were harvested at approximately 11 weeks post planting when carotenoid accumulation becomes apparent in the storage root. Storage root tissue from sixteen individual carrot roots was pooled into three one-gram tissue pools of four carrots for each genotype.
2014-08-13 | E-GEOD-49873 | biostudies-arrayexpress
Project description:Boihai Red is new strains of inter-specific hybridizing the bay scallop (Argopecten irradians irradians) with the Peruvian scallop (Argopecten purpuratus). Orange color variant of adductor muscle have been developed through successive selective breeding in this strain. In the present study, transcriptomic was conducted on orange and white adductor muscle tissues. Transcriptomic analysis showeds 416 differentially expressed genes (DEGs) were identified between white and orange adductor muscle tissues in Boihai Red Scallop, with 216 up regulated and 200 down. In DEGs, apolipophorin, CYP450 and tyrosinase were expressed highly in orange adductor muscle tissues, which related to carotenoids or melanin. It is probable that not only carotenoids, but also melanin act on orange color of adductor muscle. This study provides valuable genetic resources for understanding underlying mechanisms and pathways of adductor muscle color.
2019-04-15 | GSE122451 | GEO
Project description:Boihai Red is new strains of inter-specific hybridizing the bay scallop (Argopecten irradians irradians) with the Peruvian scallop (Argopecten purpuratus). Orange color variant of adductor muscle have been developed through successive selective breeding in this strain. In the present study,proteomic were conducted on orange and white adductor muscle tissues.Notably, 74 differentially expressed proteins (DEPs) were identified by lable free proteomics, including 36 up and 38 down regulated. In DEGs, apolipophorin, CYP450 and tyrosinase were expressed highly in orange adductor muscle tissues, which related to carotenoids or melanin. In DEPs, high expression of VPS and TIF in orange adductor muscle tissues indicated that proteins outside the carotenoid pathway might also affect carotenoid biosynthesis. In addition, RAB11A related to melanin was also expressed highly in orange adductor muscle tissues at protein level. It is probable that not only carotenoids, but also melanin act on orange color of adductor muscle. This study provides valuable genetic resources for understanding underlying mechanisms and pathways of adductor muscle color.
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Project description:Gene expression profiling reveals a potential role of Orange cells (BT-OC) in stimulating hair growth in dermal papilla cells. HFDPCs were human primary cells line, treated with 1:2000 Orange cells (BT-OC) for 48 h. Microarray gene expression profiling was conducted for three biological replicates
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Project description:Using sRNA-Seq to provide small RNA status in fruit ripening stages in sweet orange DNA methylation is an important epigenetic mark involved in many biological processes. The genome of the climacteric tomato fruit undergoes a global loss of DNA methylation due to active DNA demethylation during the ripening process. It is unclear whether the ripening of other fruits is also associated with global DNA demethylation. We characterized the single-base resolution DNA methylomes of sweet orange fruits. Compared to immature orange fruits, ripe orange fruits gained DNA methylation at over 30,000 genomic regions and lost DNA methylation at about 1,000 genomic regions, suggesting a global increase in DNA methylation during orange fruit ripening. This increase in DNA methylation was correlated with decreased expression of DNA demethylase genes. The application of a DNA methylation inhibitor interfered with ripening, indicating that the DNA hypermethylation is critical for the proper ripening of orange fruits. We found that ripening-associated DNA hypermethylation was associated with the repression of several hundred genes, such as photosynthesis genes, and with the activation of hundreds of genes including genes involved in ABA responses. Our results suggest important roles of DNA methylation in orange fruit ripening.
2018-12-28 | GSE120025 | GEO
Project description:This is a study to identify clinically relevant molecular signatures of gene expression in cervical cancer samples fro m patients in India Keywords: Cancer versus normal study
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