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GenomicsEpigenome characterization at single base-pair resolution
We have combined standard micrococcal (MNase) digestion of nuclei with a modified protocol for construction paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrap...
ORGANISM(S): Saccharomyces cerevisiae 
2011-10-26 | E-GEOD-30551 | biostudies-arrayexpress
TranscriptomicsS2_RNA_expression_Tiling_Array
modENCODE_submission_2769 This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: poly A+ RNA was isolated and used to synthesize single-stranded cDNA probes. Labeled cDNA and labeled genomic DNA were h...
ORGANISM(S): Drosophila melanogaster 
2010-11-18 | E-GEOD-25392 | biostudies-arrayexpress
TranscriptomicsKc_RNA_Expression_Tiling_Array
modENCODE_submission_2758 This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: poly A+ RNA was isolated and used to synthesize single-stranded cDNA probes. Labeled cDNA and labeled genomic DNA were h...
ORGANISM(S): Drosophila melanogaster 
2010-11-18 | E-GEOD-25387 | biostudies-arrayexpress
TranscriptomicsKc_H2Av_Knockdown_RNA_Expression_Tiling_Array
modENCODE_submission_2761 This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: poly A+ RNA was isolated and used to synthesize single-stranded cDNA probes. Labeled cDNA and labeled genomic DNA were h...
ORGANISM(S): Drosophila melanogaster 
2010-11-18 | E-GEOD-25390 | biostudies-arrayexpress
TranscriptomicsN2_Worm_Embryo_mRNA_Expression
modENCODE_submission_2762 This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: poly A+ RNA was isolated and used to synthesize single-stranded cDNA probes. Labeled cDNA and labeled genomic DNA were h...
ORGANISM(S): Caenorhabditis elegans 
2010-11-18 | E-GEOD-25391 | biostudies-arrayexpress
GenomicsDynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1)
Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped t...
ORGANISM(S): Saccharomyces cerevisiae 
2013-03-01 | E-GEOD-39430 | biostudies-arrayexpress
GenomicsDynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)
Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped t...
ORGANISM(S): Saccharomyces cerevisiae 
2013-03-01 | E-GEOD-39431 | biostudies-arrayexpress
GenomicsGenome-wide reductions in active chromatin, paused RNA Polymerase II and nucleosome turnover during heat shock
Heat shock rapidly induces expression of a small set of genes while globally repressing transcription, making it an attractive system for studying alterations in the chromatin landscape that accompany changes in gene regulation. We have characterized these changes using low-salt extraction of intact...
ORGANISM(S): Drosophila melanogaster 
2011-11-15 | E-GEOD-30755 | biostudies-arrayexpress
TranscriptomicsA native chromatin purification system for epigenomic profiling in C. elegans
We describe an in vivo chromatin purification system for genome-wide epigenetic profiling in C. elegans. In this system, we coexpressed the E. coli biotin ligase enzyme (BirA), together with the C. elegans H3.3 gene fused to BioTag, a 23-amino acid peptide serving as a biotinylation substrate for Bi...
ORGANISM(S): Caenorhabditis elegans 
2010-05-19 | E-GEOD-18898 | biostudies-arrayexpress
GenomicsTripartite organization of centromeric chromatin in budding yeast
The centromere is the genetic locus that organizes the proteinaceous kinetochore and is responsible for attachment of the chromosome to the spindle at mitosis and meiosis. In most eukaryotes, the centromere consists of highly repetitive DNA sequences that are occupied by nucleosomes containing the C...
ORGANISM(S): Saccharomyces cerevisiae 
2011-12-07 | E-GEOD-28298 | biostudies-arrayexpress
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