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ProteomicsAffinity chromatography-based identification of sRNA protein partners in Rhizobia
This project aims to identify novel protein partners of conserved trans-sRNAs in the α-proteobacterium Sinorhizobium meliloti. Trans-sRNAs (AbcR2, NfeR1 and EcpR1) were tagged at their 5’ ends with the MS2 aptamer. To identify the proteins associated with the trans-sRNAs we: i) expressed and purifie...
ORGANISM(S): Rhizobium meliloti (Ensifer meliloti) (Sinorhizobium meliloti) 
2020-10-19 | PXD006410 | Pride
Trans-srnas Ms2 aptamer Sinorhizobium meliloti Lc-ms/ms 
UnknownConservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.
Not available
S-EPMC3927594 | biostudies-literature
TranscriptomicsAnalysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing
Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. The melon research community has recently benefited from the determination of a complete draft genome sequence and the development of associated genomic tools, which have allowed us to focus on small RNAs (s...
ORGANISM(S): Cucumis melo 
2011-08-03 | E-GEOD-28653 | biostudies-arrayexpress
TranscriptomicsGeneration and characterization of a tomato DCL3 silencing mutant
DICER-like 3 (DCL3) is a major player in heterochromatic 24-nucleotide siRNA and long miRNA biogenesis and mutants have been characterized from Arabidopsis and rice. Here, a tomato DCL3 mutant was generated through the use of trans-activated artificial microRNA and characterized. Global tomato DCL3 ...
ORGANISM(S): Solanum lycopersicum 
2014-03-31 | E-GEOD-52265 | biostudies-arrayexpress
TranscriptomicsControl of RNA stability by NrrF, an iron-regulated small RNA in Neisseria gonorrhoeae.
Regulation of gene expression by small non-coding RNAs (sRNAs) plays a critical role in bacterial response to physiological stresses. NrrF, a trans-acting sRNA in Neisseria meningitidis and Neisseria gonorrhoeae, has been shown in the meningococcus to indirectly control, in response to iron (Fe) av...
ORGANISM(S): Neisseria gonorrhoeae 
2013-09-27 | E-GEOD-48526 | biostudies-arrayexpress
Genomics
Host AGO1-associated trans-kingdom sRNAs
PRJNA794992 | ENA
TranscriptomicsSmall RNAs as important regulators for the hybrid vigour of super-hybrid rice
Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature ...
ORGANISM(S): Oryza sativa 
2014-08-17 | E-GEOD-51468 | biostudies-arrayexpress
TranscriptomicsConvolutional neural network modelling: advancing identification of true mRNA cleavage sites
Degradome sequencing is commonly used to generate high-throughput information on mRNA cleavages by small RNAs. Here we developed an extension module based on a deep learning convolutional neural network (CNN) in a machine learning environment to discriminate false from true cleavage sites applied on...
ORGANISM(S): Solanum tuberosum Phytophthora infestans 
2021-05-05 | GSE163382 | GEO
UnknownCompensatory sequence variation between trans-species small RNAs and their target sites.
Not available
S-EPMC6917502 | biostudies-literature
TranscriptomicsSmall RNAs profiling by using microarray with custom-designed probes
We designed a group of probes for detection of known and some putative E. coli sRNAs and included them in a commercial microarray containing a standard set of probes developed by Agilent Technologies for hybridization with E. coli transcripts. To assess the potential of the re-designed microarray to...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2016-01-04 | E-MTAB-3329 | biostudies-arrayexpress
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