Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Solanum lycopersicum

ABSTRACT: High-throughput sequencing of small RNAs in Solanum lycopersicum

OTHER RELATED OMICS DATASETS IN: E-MTAB-4812

PROVIDER: PRJNA147705 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

The role of small RNAs on phenotypes in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium

Project description:we found the expression levels of 76 known miRNAs were highly variable between the reciprocal hybrids through the high-throughput sequencing of small RNAs small RNA sequencing were performed in Solanum lycopersicum, S. pimpinellifolium and their reciprocal hybrids

2014-10-10 | E-GEOD-62196 | biostudies-arrayexpress

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

Solanum lycopersicum

Project description:High-throughput pyrosequencing of endogenous small RNAs from Solanum lycopersicum leaf and fruit

| PRJNA113341 | ENA

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

Project description:Solanum lycopersicum RNA degradome sequencing

2012-08-29 | GSE22236 | GEO

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

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

2021-02-27 | GSE164382 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum Axillary bud Transcriptomes

Project description:RNA sequencing in tomato for detect mRNA expression of Solanum lycopersicum Axillary bud.The two cultivars (monomaker, raceme) at Axillary bud for transcriptome sequencing

2021-12-31 | GSE164164 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum Flower Transcriptomes

Project description:RNA sequencing in tomato for detect mRNA expression of Solanum lycopersicum flower.The two cultivars (monomaker, raceme) had three different flowering stages (budlet, Flower bud, Full bloom) for transcriptome sequencing

2021-08-11 | GSE163914 | GEO

High-throughput sequencing of small RNAs in Solanum lycopersicum

2011-09-30 | GSE32470 | GEO

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.

2017-05-11 | MSV000081074 | MassIVE

High-throughput sequencing of small RNAs in Solanum lycopersicum

Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Solanum licopersicum tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study. Small RNA libraries were derived from leaves, flowers and fruit of Solanum licopersicum. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Harry Klee for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

2011-09-29 | E-GEOD-32470 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data