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TranscriptomicsTranscriptome and methylome interactions in rice hybrids
This research reports genome-wide measurements of genetic and epigenetic patterns of inheritance through an integrative analysis of BS-seq, RNA-seq, and siRNA-seq data in two inbred parents of the Nipponbare (NPB) and Indica (93-11) variety of rice and their hybrid offspring. We generated integrativ...
ORGANISM(S): Oryza sativa Indica Group 
2012-07-10 | E-GEOD-38480 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of rice roots and tips in early development by massive parallel sequencing
Despite the major physiological dissimilarities between roots and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. Japonica) mature root tissue and root tips was monitored using mRNA-Seq at 2 time...
ORGANISM(S): Oryza sativa Japonica Group 
2012-01-12 | E-GEOD-30367 | 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
TranscriptomicsDifferentiated Truncation and Uridylation Patterns of miRNAs in Arabidopsis and Rice hen1 Mutants Suggest miRNAs May Re-program RISC
miRNA levels depend on both biogenesis and turnover. The methyltransferase HEN1 stabilizes plant miRNAs, animal piRNAs, and siRNAs in both kingdoms via 3' terminal methylation. Loss of HEN1 in plants results in non-templated oligo-uridylation and accelerated degradation of miRNAs. In hen1 mutants fr...
ORGANISM(S): Arabidopsis thaliana 
2013-07-22 | E-GEOD-35562 | biostudies-arrayexpress
TranscriptomicsTranscriptional analysis of giant cells induced by root knot nematodes in rice
Biotrophic plant pathogens have evolved sophisticated strategies to manipulate their host. They derive all of their nutrients from living plant tissues, by making intimate contact with their host while avoiding a resistance response. Rice is one of the most important crop plants worldwide and an exc...
ORGANISM(S): Oryza sativa Japonica Group 
2013-08-07 | E-GEOD-43577 | biostudies-arrayexpress
TranscriptomicsSystemic suppression of the rice shoot metabolism upon root rot nematode infection
Rice (Oryza sativa L.) is one of the most important staple foods in the world, feeding more than 50% of the human population. One of its most damaging pathogens, with major impact on rice yield, is the migratory root rot nematode Hirschmanniella oryzae. In comparison with the existing knowledge on t...
ORGANISM(S): Oryza sativa Japonica Group 
2015-05-18 | E-GEOD-57707 | biostudies-arrayexpress
TranscriptomicsTranscriptional reprogramming by root knot and migratory nematode infection in rice
In this study a comparison was made between the local transcriptional changes at two time points upon root knot (Meloidogyne graminicola) and migratory nematode (Hirschmanniella oryzae) infection in rice. Using mRNA-Seq we have characterized specific and general responses of the root challenged with...
ORGANISM(S): Oryza sativa Japonica Group 
2013-01-10 | E-GEOD-35843 | biostudies-arrayexpress
UnknownTranscriptome and methylome interactions in rice hybrids.
Not available
S-EPMC3409791 | biostudies-literature
ProteomicsDisruption of proteome by an oncogenic fusion kinase alters metabolism in fibrolamellar hepatocellular carcinoma
Fibrolamellar hepatocellular carcinoma (FLC) is a usually lethal primary liver cancer driven by a somatic dysregulation of protein kinase A. We show that the proteome of FLC tumors is distinct from that of adjacent nontransformed tissue. These changes can account for some of the cell biological and ...
ORGANISM(S): Homo sapiens (Human) 
2024-10-17 | PXD046905 | Pride
Proteomics Fibrolamellar hepatocellular carcinoma Flc 
UnknownExperimental rice seed aging under elevated oxygen pressure: Methodology and mechanism.
Not available
S-EPMC9751813 | biostudies-literature
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