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TranscriptomicsFunctional analysis of Arabidopsis ARGONAUTE1 using a slicer-defective mutant: Small RNA immunoprecipitation
The Arabidopsis ARGONAUTE (AGO) protein AGO1 associates with microRNA (miRNA) and specific classes of short-interfering RNA (siRNA). AGO1-small RNA complexes recognize target RNA transcripts through base-pairing interactions and inhibit translation of target RNAs through endonucleolytic cleavage (sl...
ORGANISM(S): Arabidopsis thaliana 
2012-09-28 | E-GEOD-40258 | biostudies-arrayexpress
TranscriptomicsRoles and Programming of Arabidopsis ARGONAUTE Proteins During Turnip Mosaic Virus Infection
AGO protein immunoprecipitation was combined with high-throughput sequencing of associated small RNAs. AGO2, AGO10, and to a lesser extent AGO1 were shown to associate with siRNAs derived from silencing suppressor (HC-Pro)-deficient TuMV-AS9, but not with siRNAs derived from wild-type TuMV. Co-immun...
ORGANISM(S): Arabidopsis thaliana 
2015-04-06 | E-GEOD-64911 | biostudies-arrayexpress
TranscriptomicsComputational and Analytical Framework for Small RNA Profiling by High-Throughput Sequencing (reproducibility)
The purpose of this work was to describe a computational and analytical methodology for profiling small RNA by high-throughput sequencing. The datasets here were used to assess the reproducibility of small RNA datasets produced using Illumina sequencing-by-synthesis technology (SBS). We analyzed th...
ORGANISM(S): Arabidopsis thaliana 
2009-06-02 | E-GEOD-14694 | biostudies-arrayexpress
TranscriptomicsComputational and Analytical Framework for Small RNA Profiling by High-Throughput Sequencing (standards)
The purpose of this work was to describe a computational and analytical methodology for profiling small RNA by high-throughput sequencing. The datasets here were used to develop synthetic oligoribonucleotides as spike-in standards. We assessed the use of synthetic oligoribonucleotide standards as s...
ORGANISM(S): Arabidopsis thaliana 
2009-06-02 | E-GEOD-14695 | biostudies-arrayexpress
TranscriptomicsArabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology
To determine the extent to which the major small RNA pathways functions across the Arabidopsis thaliana genome, small RNA populations from several tissues of wild-type (wt) and mutant plants were amplified by RT-PCR and sequenced using high-throughput 454 sequencing technology. Keywords: small RNAs,...
ORGANISM(S): Arabidopsis thaliana 
2007-02-01 | E-GEOD-6682 | biostudies-arrayexpress
TranscriptomicsFunctional analysis of Arabidopsis ARGONAUTE1 using a slicer-defective mutant: Transcript immunoprecipitation
The Arabidopsis ARGONAUTE (AGO) protein AGO1 associates with microRNA (miRNA) and specific classes of short-interfering RNA (siRNA). AGO1-small RNA complexes recognize target RNA transcripts through base-pairing interactions and inhibit translation of target RNAs through endonucleolytic cleavage (sl...
ORGANISM(S): Arabidopsis thaliana 
2012-09-28 | E-GEOD-40256 | biostudies-arrayexpress
TranscriptomicsGlobal identification of Arabidopsis thaliana ARGONAUTE1-associated small RNA.
Small RNA from total RNA (input fraction) and immunoprecipitated HA-AGO1-complexes (IP fraction) were identified using high-throughput sequencing-by-synthesis. Two replicate input fraction samples were used as controls for two replicate IP fraction samples. Total RNA from input fractions and small R...
ORGANISM(S): Arabidopsis thaliana 
2010-06-21 | E-GEOD-22252 | biostudies-arrayexpress
TranscriptomicsMIRNA Gene Evolution in Arabidopsis lyrata and Arabidopsis thaliana: Illumina sequencing
Deep sequencing of small RNA from three closely related brassicaceae A. thaliana, A. lyrata and Capsella rubella was done to systematically analyze the evolution of MIRNA genes and their targets. Small RNA were extracted from total RNA by size fractionation and converted to DNA amplicons by serial a...
ORGANISM(S): Arabidopsis lyrata 
2010-05-14 | E-GEOD-20660 | biostudies-arrayexpress
TranscriptomicsPhytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs: Phytophthora infestans small RNA
Deep sequencing of small RNAs from three Phytophthora species, P. infestans, P. ramorum and P. sojae, was done to systematically analyze small RNA-generating components of Phytophthora genomes. We found that each species produces two distinct small RNA populations that are predominantly 21- or 25-nu...
ORGANISM(S): Phytophthora infestans 
2013-10-21 | E-GEOD-50030 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of Arabidopsis Col-0, ARF10 and mARF10 plants to identify genes regulated by ARF10 in germinating seeds
The expression profiles were determined using Affymetrix ATH1 arrays. Comparisons among the Col-0, ARF10 and mARF10 sample groups allow the identification of genes regulated by ARF10. Experiment Overall Design: Germinating seeds (22 hr imbibition) from three independent biological replicates of Col-...
ORGANISM(S): Arabidopsis thaliana 
2008-06-15 | E-GEOD-7227 | biostudies-arrayexpress
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