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Solanum melongena

ABSTRACT: Development of a Multi-parent Advanced Generation Inter-Cross (MAGIC) population in common eggplant

PROVIDER: PRJNA392603 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5796640.fastq.gz	Fastqsanger.gz
	SRR5796640_1.fastq.gz	Fastqsanger.gz
	SRR5796640_2.fastq.gz	Fastqsanger.gz
	SRR5796641_1.fastq.gz	Fastqsanger.gz
	SRR5796641_2.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of Eggplant (Solanum melongena L.) cv. PPL during fruit development and ripening.

2014-02-14 | GSE44182 | GEO

Transcriptome analysis of Eggplant (Solanum melongena L.) cv. PPL during fruit development and ripening.

Project description:Transcriptome analysis of Eggplant cv. PPL during fruit development at 0, 5, 10, 20 and 50 dpa. Eggplant is third most important solanaceae crop species after potato and tomato. It is a versatile crop adapted to different agro-climatic regions and can be grown throughout the year. Unripe eggplant fruit is consumed as cooked vegetable in various ways. It is low in calories and fats, contains mostly water, some protein, fibre and carbohydrates. To decipher molecular mechanisms involved in fruit development eggplant fruit were collected at 0, 5, 10, 20 and 50 dpa and gene expression profiles were analyzed using Affymetrix tomato GeneChip Genome array. Eggplant plants were was grown under controlled conditions in glasshouse. Flowers were hand-pollinated at anthesis and samples were collected at 0, 5, 10, 20 and 50 days post anthesis (dpa). Total RNA was isolated using SpectrumTM Plant Total RNA kit (Sigma, USA) according to the manufacturerM-bM-^@M-^Ys protocol. Affymetrix tomato GeneChip Genome array (Affymetrix, USA) having 10,000 probe sets was used for transcriptome analysis. Three biological replicates were maintained to test the reproducibility and quality of the chip hybridization. cDNA labeling, array hybridization, staining and washing procedures were carried out as described in the Affymetrix protocols. CEL files having estimated probe intensity values were analyzed with GeneSpring GX-11.5 software (Agilent Technologies, USA) to get differentially expressed transcripts. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

2014-02-14 | E-GEOD-44182 | biostudies-arrayexpress

Spatial metabolomics of eggplant (Solanum melongena)

Project description:Spatial metabolomics of eggplant (Solanum melongena). This analysis comprehends different regions of the plant, including fruit, leaf, stem, and root.

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Cicer arietinum

Project description:Chickpea multi-parent advanced generation intercross (MAGIC) population

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Transcriptomes for hybrids (F1s) between 18 Arabidopsis thaliana parents of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource

2014-03-01 | GSE55482 | GEO

Genome-wide identification of eggplant (Solanum melongena L.) miRNAs and their targets reveals differential regulation of heterostyly [Seq]

Project description:MicroRNAs (miRNAs), a class of endogenous, non-coding, ~21 nucleotide RNAs, regulate the expression of their target genes by mRNA cleavage or translation inhibition. In plants, miRNAs have been demonstrated to play crucial roles in regulating diverse cellular, physiological, and developmental processes. The identification of all the miRNAs is not yet complete; there are no studies on their possible links with the difference in heterostyly observed in eggplant (Solanum melongena L.).

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Genome-wide identification of eggplant (Solanum melongena L.) miRNAs and their targets reveals differential regulation of heterostyly [Array]

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A high temperature RNA-seq dataset for studies of gene expression variation in the MAGIC line resource of Arabidopsis thaliana

Project description:To understand expression phenotypes in Arabidopsis thaliana at high temperature, a set of the Multiparent Advanced Generation Inter-Cross (MAGIC) recombinant inbred lines were grown under long day conditions (16 hours light: 8 hours dark) at 20˚C and then shifted to 30˚C for 48 hours. RNA was collected at the 4th true leaf stage, and RNA-seq data was generated using the Illumina method. The MAGIC lines included are largely a subset of lines for which comparable RNA-seq data was collected at a constant 20˚C (allowing the same genotypes to be compared at 20˚C and after the high temperature shift at approximately the same developmental stage and under otherwise the same growth conditions). The read data for the analogous low temperature study can be found under GEO submission GSE94107.

2017-04-22 | GSE96812 | GEO

E-GEOD-55482

Project description:Transcriptomes for hybrids (F1s) between 18 Arabidopsis thaliana parents of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource

2015-12-02 | E-GEOD-55482 | ExpressionAtlas

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Project description:We produced RNA-Seq reads from messenger RNA isolated from aerial seedling tissue for 9 hybrids (F1s) generated by crossing in a pairwise manner 18 of the founding accessions (inbred strains) of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource for Arabidopsis thaliana (see Gan et al. 2011. Nature, 477:419-23 for a description of the MAGIC genetic mapping resource). The resulting RNA-Seq data provides a resource to assess allele-specific gene expression between A. thaliana accessions. With 18 of the MAGIC parental inbred accessions (Bur-0, Can-0, Col-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, and Zu-0) crosses were performed to generate 9 sets of F1 progeny from which RNA was extracted with biological replication (three replicates) and for which mRNA-seq was performed to generate strand-specific reads. Library construction and sequencing was performed such that each set of biological replicates were sequenced as a pool (with 9-plex barcoding; each 9-plex was run on two HiSeq lanes).

2014-03-01 | E-GEOD-55482 | biostudies-arrayexpress

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