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TranscriptomicsCharacterization of technical variation in ChIP-on-chip studies
Analysis of technical variance of ChIP-on-Chip studies by characterization of Myc-binding in HL60 cells. Keywords: Chip-on-chip Fully-blocked study of technical variance in Myc-binding in HL60 cells. Two different antibodies were used to generate 6 biologically independent replicates each. Each repl...
ORGANISM(S): Homo sapiens 
2008-10-31 | E-GEOD-8448 | biostudies-arrayexpress
Transcriptomicsc-Myc binding in HL60 cells
Analysis of technical variance of ChIP-on-Chip studies by characterization of Myc-binding in HL60 cells. Keywords: Chip-on-chip Characterization of c-Myc binding in HL60 cells. Thirteen biologically independent replicates of growing HL60 cells were subjected to ChIP with an N-terminal c-Myc antibod...
ORGANISM(S): Homo sapiens 
2010-05-17 | E-GEOD-8447 | biostudies-arrayexpress
TranscriptomicsSpike-in Experiment for ChIP-chip Simulation
The most widely-used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms and analysis algorithms in a simulated ChIP-chip experiment. M...
ORGANISM(S): Homo sapiens 
2010-05-22 | E-GEOD-9732 | biostudies-arrayexpress
TranscriptomicsPromoter proximal pausing and its regulation by c-Myc in embryonic stem cells: ChIP-chip
Recruitment of the RNA Polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA binding transcription factors is well recognized as a key regulatory step in gene expression. We describe here evidence that promoter-proximal pausing is a general feature of transcription ...
ORGANISM(S): Mus musculus 
2010-04-02 | E-GEOD-20529 | biostudies-arrayexpress
TranscriptomicsChip-chip analysis of C. glutamicum SigC
Bacteria modify expression of different types of terminal oxidase in response to oxygen availability. Corynebacterium glutamicum, a facultative anaerobic bacterium in Actinobacteria, possesses aa3-type cytochrome c oxidase and cytochrome bd-type quinol oxidase, the latter of which is induced upon ox...
ORGANISM(S): Corynebacterium glutamicum 
2016-08-22 | E-GEOD-72452 | biostudies-arrayexpress
TranscriptomicsChIP-chip analysis of NFI-1 in wildtype (N2) mixed stage C. elegans
The conserved Nuclear Factor I (NFI) family of transcription factors is unique to animals and essential for mammalian development. The C. elegans genome encodes a single NFI family member, whereas vertebrate genomes encode four distinct NFI protein subtypes (A, B, C, and X). NFI-1 deficient worms ex...
ORGANISM(S): Caenorhabditis elegans 
2009-01-30 | E-GEOD-13918 | biostudies-arrayexpress
TranscriptomicsStress-dependent CHIP/Daxx interaction suppresses the p53 apoptotic program
Our previous studies have implicated CHIP as a co-chaperone/ubiquitin ligase, whose activities yield protection against stress-induced apoptotic events. In this report, we demonstrate a stress-dependent interaction between CHIP (carboxyl terminus of Hsp70-interacting protein) and Daxx, death domain-...
ORGANISM(S): Mus musculus 
2010-04-03 | E-GEOD-14339 | biostudies-arrayexpress
TranscriptomicsChip-chip from E. coli MG1655 cells with different methods to detect SeqA and σ32 binding and causes of high background
Reinvestigation of the chromatin immunoprecipitation procedure led us to discover four causes of high background: non-unique sequences, incomplete reversion of crosslinks, washing with spin-columns and insufficient RNase treatment. We used a publishd method giving a high background signal and a modi...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2010-07-12 | E-GEOD-19053 | biostudies-arrayexpress
TranscriptomicsChip-chip from C-33 cells expressing FLAG-HPV1 E2 with FLAG-HPV1 E2
HPV1 E2 binds with Brd4 to host mitotic chromosomes. To identify the targets, chromatin was prepared from mitotic C-33 cells expressing HPV1 E2, and analyzed by ChIP-chip analysis for binding to a portion of the human genome. E2 and Brd4 bind to active promoters in interphase C-33 cells (Jang et al....
ORGANISM(S): Homo sapiens 
2014-04-14 | E-GEOD-52312 | biostudies-arrayexpress
TranscriptomicsDeconvolution of ChIP-chip MBF occupancies reveals the temporal recruitment of Rep2 at the MBF-target genes
Deconvolution analysis using Rpb1 ChIP-chip results distinguishes the Cdc10 bindings at the Rpb1-poor loci (promoters) from those at the Rpb1-rich loci (intragenic sequences). Importantly, Res1 binding at the Rpb1-poor loci, but not at the Rpb1-rich loci, are dependent on the Cdc10 function, suggest...
ORGANISM(S): Schizosaccharomyces pombe 
2010-11-26 | E-GEOD-9912 | biostudies-arrayexpress
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