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MicroRNA-target RNA pairs revealed by Parallel analysis of RNA ends in Solanum lycopersicum

ABSTRACT: Solanum lycopersicum RNA degradome sequencing

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE22236 | GEO | 2012/08/29

SECONDARY ACCESSION(S): PRJNA128851

REPOSITORIES: GEO

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microRNA-target RNA pairs revealed by Parallel analysis of RNA ends in Solanum lycopersicum

Project description:Solanum lycopersicum RNA degradome sequencing Isolated polyadenylated RNA from total RNA extracts of Solanum lycopersicum, were ligated to 5'-adapter that includes an MmeI recognition site. The ligated products were purified again, reverse transcribed and cleaved with MmeI. The 5' fragments were purified from gel and ligated to a 3'- dsDNA adapter and PCR amplified. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

2012-08-29 | E-GEOD-22236 | biostudies-arrayexpress

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Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum bud and flower Transcriptomes

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Spectral library of Solanum lycopersicum for SWATH-MS

Project description:A spectral library was built for Solanum lycopersicum. The spectral library allows reproducible quantification for thousands of peptides per SWATH-MS analysis. Proteins from Solanum lycopersicum pericarp were digested with trypsin using in-gel digestion and the peptides were fractionated by high-pH reverse phase chromatography. HRM peptides were spiked into the peptides mixture and each fraction was injected on a Sciex TripleTOF 6600 mass spectrometer fitted with microflow set-up. The resulting .wiff files were analysed using MaxQuant and Spectronaut.

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Solanum lycopersicum

Project description:Solanum lycopersicum

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Solanum lycopersicum Transcriptome or Gene expression

Project description:Lines nearly isogenic for fw3.2 in the cultivated background Solanum lycopersicum c.v. Yellow Stuffer were grown in the greenhouse in a completely randomized design. fw3.2 (ys) and fw3.2 (wt) are NILs carrying cultivated and wild alleles for fw3.2 locus. Young flower buds were harvested. For each sample, three replicates were used. RNA was extracted using Trizol and Stand-specific libraries were prepared from total RNA and sequences of 51 bp were generated on an Illumina HiSeq2000.

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