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TranscriptomicsDNA methylation in Arabidopsis thaliana
DNA methylation in wild type bolting plants, wild type seedlings, and ddm1 seedlings. The purpose of the McrBC methylation microarray assay is to determine which regions of a genome are methylated versus those that are unmethylated in a single Arabidopsis thanliana genotype. McrBC is a methylation-s...
ORGANISM(S): Arabidopsis thaliana 
2010-06-09 | E-GEOD-1355 | biostudies-arrayexpress
TranscriptomicsHistone methylation in wild type and ddm1 Arabidopsis thaliana seedlings
Histone 3 lysine 4 and histone 3 lysine 9 methylation in wild type and ddm1 Arabidopsis thaliana seedlings. The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arab...
ORGANISM(S): Arabidopsis thaliana 
2010-06-09 | E-GEOD-1356 | biostudies-arrayexpress
TranscriptomicsmRNA levels in Wild-type versus ddm1 Arabidopsis thaliana
mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings and bolting plants. Features found to be significantly enriched for DNA methylation were determined. This SuperSeries is composed of the following subset Series: GSE1324: EV23+24 mRNA levels in Wild-type versus ddm1/+ backcross bo...
ORGANISM(S): Arabidopsis thaliana 
2010-06-09 | E-GEOD-1354 | biostudies-arrayexpress
TranscriptomicsIn Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts
Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown a...
ORGANISM(S): Arabidopsis thaliana 
2014-02-03 | E-GEOD-45549 | biostudies-arrayexpress
TranscriptomicsSmall RNA sequences from Schizosaccharomyces japonicus
Small interfering RNAs (siRNAs) are known to be involved in both transposon silencing and centromere function, leading us to investigate the interplay between these two roles in the Schizosaccharomyces lineage. In S. pombe, the centromeric repeats produce dicer-dependent siRNAs that are required for...
ORGANISM(S): Schizosaccharomyces japonicus 
2011-03-09 | E-GEOD-27837 | biostudies-arrayexpress
TranscriptomicsArabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state
DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about replication programs in plants. We u...
ORGANISM(S): Arabidopsis thaliana 
2011-07-06 | E-GEOD-30433 | biostudies-arrayexpress
TranscriptomicsSpreading of heterochromatin is limited to specific families of maize retrotransposons
Transposable elements have the potential to act as controlling elements to influence the expression of genes. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of the transposable element and influence the chromatin state of neighboring low-copy sequences. ...
ORGANISM(S): Zea mays 
2012-11-26 | E-GEOD-39460 | biostudies-arrayexpress
TranscriptomicsProfiling the transcriptome of Thalassiosira pseudonana under environmentally relevant growth conditions
T. pseudonana gene-specific arrays were used for differential gene expression. Seven hundred nine genes were differentially expressed by more than 2-fold (Bayesian t-test, p< 0.001) under at least one growth-limiting condition relative to nutrient-replete conditions. A striking result of the hierarc...
ORGANISM(S): Thalassiosira pseudonana CCMP1335 
2010-05-26 | E-GEOD-9660 | biostudies-arrayexpress
TranscriptomicsEpigenetic reprogramming and small RNA silencing of transposable elements in pollen.
The mutagenic activity of transposable elements (TEs) is suppressed by epigenetic silencing and small interfering RNAs (siRNAs), especially in gametes that would transmit transposed elements to the next generation. In pollen from the model plant Arabidopsis, we show that TEs are unexpectedly reactiv...
ORGANISM(S): Arabidopsis thaliana 
2014-09-04 | E-GEOD-61028 | biostudies-arrayexpress
TranscriptomicsProfiling the transcriptome of Thalassiosira pseudonana under silicon replete and deplete growth.
T. pseudonana tiling arrays were used to validate gene models and to predict new genes in the genome of this diatom. The tiling array data validated transcription of about 41% (4,653) of the 11,390 computationally predicted genes. An additional 1,132 transcripts were identified that did not correspo...
ORGANISM(S): Thalassiosira pseudonana CCMP1335 
2010-05-26 | E-GEOD-9661 | biostudies-arrayexpress
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