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Transcriptome Analysis

ABSTRACT: Transcriptome Analysis of carrot

PROVIDER: PRJEB4558 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR338560_1.fastq.gz	Fastqsanger.gz
	ERR338560_2.fastq.gz	Fastqsanger.gz
	ERR338561_1.fastq.gz	Fastqsanger.gz
	ERR338561_2.fastq.gz	Fastqsanger.gz

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Transcriptome evaluation of gene expression changes during carotenoid accumulation in the storage root of carrot (Daucus carota)

2014-08-13 | GSE49873 | GEO

Transcriptome evaluation of gene expression changes during carotenoid accumulation in the storage root of carrot (Daucus carota)

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

Comparative Transcriptomics Analysis of Red (Wild) and Orange (Modified) Carrots Available in India

Project description:We provide a comparative transcriptomics analysis between wild (red or Delhi) and modified (orange or hybrid) carrot roots available in India.

2021-12-31 | GSE179859 | GEO

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Intestinal Microbiome, Oral Microbiome, and Whole Blood Transcriptome Analyses in Gastrointestinal Malignancies

Project description:The primary objective of this prospective observational study is to characterize the gut and oral microbiome as well as the whole blood transcriptome in gastrointestinal cancer patients and correlate these findings with cancer type, treatment efficacy and toxicity. Participants will be recruited from existing clinical sites only, no additional clinical sites are needed.

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Transcriptome analysis of the transgenic and non-transgenic fleshy roots

Project description:Effect of betanin synthesis on the metabolism of transgenic carrot. Betalain is a natural pigment with important nutritional value and broad application prospects. Previously, we produced betanin biosynthesis transgenic carrots via expressing optimized genes CYP76AD1S, cDOPA5GTS and DODA1S. Betanin can accumulate throughout the whole transgenic carrots. But the effects of betanin accumulation on the metabolism of transgenic plants and whether it produces unexpected effects are still unclear.

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Transcriptome analysis reveals candidate genes related to anthocyanin biosynthesis in different carrot genotypes and tissues

Project description:Transcriptome analysis reveals candidate genes related to anthocyanin biosynthesis in different carrot genotypes and tissues

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Project description:Cultivated carrot (Daucus carota L. ssp. sativus) was domesticated from wild carrot (Daucus carota L. ssp. carota) with radical different traits. The aim of this study was to compare the root transcriptomes between cultivated and wild carrots for SNP discovery, inferring domestication process, and identifying domestication genes. Six cultivated carrots representing main European carrot root types and five wild carrot populations from widely dispersed sites were used. The root transcriptomes were sequenced with multiplexing paried-end sequencing in Illumina Genome Analyzer IIx.

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Project description:Carrot root transcriptome

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Transcriptome analysis reveals candidate genes related to anthocyanin biosynthesis in different carrot genotypes and tissues

Project description:Taproots of different carrot genotypes were used to identify the candidate genes related to anthocyanin synthesis with particular focus on R2R3MYB, bHLH transcription factors, and glutathione S-transferase gene (GST). The RNA-sequencing analysis (RNA-Seq) showed that DcMYB6 and DcMYB7 had genotypic dependent expressed and they are likely involved in the regulation of anthocyanin biosynthesis. They were specifically upregulated in solid black taproots, including both black phloem and xylem. DcbHLH3 (LOC108204485) was upregulated in all black samples compared with the orange ones. We also found that GST1 (LOC108205254) might be an important anthocyanin transporter, and its upregulated expression resulted in the increasing of vacuolar anthocyanin accumulation in black samples.

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