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TranscriptomicsA Comparison of microarray and MPSS Technology Platforms for Expression Analysis of Arabidopsis
A comparison of microarray and MPSS technologies can help to establish the metrics for data comparisons across these technology platforms and determine some of the factors affecting the measurement of mRNA abundances using different platforms. Here, different Treatments/Conditions based on differen...
ORGANISM(S): Arabidopsis thaliana 
2007-09-14 | E-GEOD-8994 | biostudies-arrayexpress
GenomicsPlants regenerated from tissue culture contain stable epigenome changes in rice
Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several transgenic rice lines. We found that all tested transgenic plan...
ORGANISM(S): Oryza sativa Japonica Group 
2013-03-26 | E-GEOD-42410 | biostudies-arrayexpress
TranscriptomicsDeep Transcriptional Profiling of Rice Using Illumina's Sequencing By Synthesis Technology
Identification of all expressed transcripts in a sequenced genome is essential both for genome analysis and for realization of the goals of systems biology. We used the transcriptional profiling technologies like M-bM-^@M-^Xmassively parallel signature sequencing (MPSS)M-bM-^@M-^Y and M-bM-^@M-^XSeq...
ORGANISM(S): Oryza sativa 
2011-06-22 | E-GEOD-25596 | biostudies-arrayexpress
TranscriptomicsGenomic and genetic characterization of rice Cen3 reveals evolutionary remnants of a complex centromere (mRNA data)
The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most muticellular eukaryotes, centromeres are composed of long tracks of satellite repeats that are recalcitrant to sequencing and fine scale genetic mapping. Here we report ...
ORGANISM(S): Oryza sativa 
2006-05-26 | E-GEOD-4920 | biostudies-arrayexpress
TranscriptomicsSmall RNA identification in Arabidopsis thaliana using modified MPSS
Small RNAs play important regulatory roles in most eukaryotes but only a small proportion of these molecules have been identified. We sequenced more than two million small RNAs from seedlings and the inflorescence of the model plant Arabidopsis thaliana. Known and new miRNAs were among the most abun...
ORGANISM(S): Arabidopsis thaliana 
2005-09-02 | E-GEOD-3008 | biostudies-arrayexpress
TranscriptomicsGenome-wide analysis for rice small RNAs by MPSS
Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ~240 miRNAs have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes. Among these, ...
ORGANISM(S): Oryza sativa 
2008-02-14 | E-GEOD-10523 | biostudies-arrayexpress
TranscriptomicsStructural Variant of a Tandem Repeat-containing Silencer Locus Reveals Distinct Pol II and Pol IV-dependent Pathways of siRNA Biogenesis
We used a two-component transgene system to study the RNA-dependent DNA methylation (RdDM) and transcriptional gene silencing (TGS) in Arabidopsis. By profiling the small RNA population in  mutants defected in RdDM or RNA polymerase II-transcribed trigger for generating silencing siRNA, we investiga...
ORGANISM(S): Arabidopsis thaliana 
2014-08-05 | E-GEOD-47852 | biostudies-arrayexpress
TranscriptomicsGenomic and genetic characterization of rice Cen3 reveals evolutionary remnants of a complex centromere (small RNA data)
The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most muticellular eukaryotes, centromeres are composed of long tracks of satellite repeats that are recalcitrant to sequencing and fine scale genetic mapping. Here we report ...
ORGANISM(S): Oryza sativa 
2006-05-26 | E-GEOD-4912 | biostudies-arrayexpress
TranscriptomicsThe dicerlike1 homologue, fuzzy tassel, is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize
We have characterized a maize mutant, fuzzy tassel (fzt) with striking inflorescence and pleiotropic defects. fzt contains a mutation in the maize dicer-like1 homolog, a key enzyme required for microRNA (miRNA) biogenesis. By profiling the small RNA population in fzt mutants, we investigated the imp...
ORGANISM(S): Zea mays 
2015-02-20 | E-GEOD-52879 | biostudies-arrayexpress
TranscriptomicsSmall RNA SBS signatures identified from maize using Illumina's SBS technology
Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. Recent work has demonstrated that the maize MEDIATOR OF PARAMUTATION1 (mop1) gene is a predicted ortholog of the Arabidopsis RDR2 gene. The mop1 gene is required for establishment of pa...
ORGANISM(S): Zea mays 
2008-09-30 | E-GEOD-12173 | biostudies-arrayexpress
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