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Unknown,Transcriptomics,Genomics,Proteomics

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Solanum lycopersicumTranscriptome or Gene expression

ABSTRACT: Gene expression in wild-type fruit. Strand-specific RNA-Seq data was used to calculate the gene expression value (RPKM) in four wild-type fruit developmental stages including immature fruit at 17DPA, mature green fruit (seeds development completes) at 39DPA, breaker fruit (onset of ripening) at 42DPA and fully ripe fruit at 52DPA. For each sample, two to four biological replicates were sequenced. Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

INSTRUMENT(S): Illumina Genome Analyzer II

ORGANISM(S): Solanum lycopersicum

SUBMITTER: Silin Zhong

PROVIDER: E-MTAB-4818 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening.

Zhong Silin S Fei Zhangjun Z Chen Yun-Ru YR Zheng Yi Y Huang Mingyun M Vrebalov Julia J McQuinn Ryan R Gapper Nigel N Liu Bao B Xiang Jenny J Shao Ying Y Giovannoni James J JJ

Nature biotechnology 20130127 2

Ripening of tomato fruits is triggered by the plant hormone ethylene, but its effect is restricted by an unknown developmental cue to mature fruits containing viable seeds. To determine whether this cue involves epigenetic remodeling, we expose tomatoes to the methyltransferase inhibitor 5-azacytidine and find that they ripen prematurely. We performed whole-genome bisulfite sequencing on fruit in four stages of development, from immature to ripe. We identified 52,095 differentially methylated re ...[more]

PMID: 23354102

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