Dataset Information


A comparison of high density oligonucleotide and PCR-based array platforms for chIP chip in yeast

ABSTRACT: ChIP chip data was obtained for the factors Tec1, Ste12 and Sok2 in S. cerevisiae using high density oligonucleotide arrays. This data was then compared to results obtained previously for the same factors under the same growth conditions but using spotted PCR arrays (Borneman et al Genes Dev 2006). This showed the high density arrays to be more reproducible using fewer numbers of replicates. In addtion, the high density arrays provided increased accuracy, sensitivity and reproducibity when compared to the PCR arrays. Keywords: ChIP-chip Overall design: ChIP chip was performed for three factors, Tec1, Ste12 and Sok2. For each factor, 3 biological replicates were performed, with one replicate for each factor treated as a dye swap.

INSTRUMENT(S): Snyder - Nimblegen S.cerevisiae WGT 50-60; 50-120

SUBMITTER: Anthony R Borneman  

PROVIDER: GSE4450 | GEO | 2006-12-13



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Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.

Borneman Anthony R AR   Zhang Zhengdong D ZD   Rozowsky Joel J   Seringhaus Michael R MR   Gerstein Mark M   Snyder Michael M  

Functional & integrative genomics 20070719 4

In recent years, techniques have been developed to map transcription factor binding sites using chromatin immunoprecipitation combined with DNA microarrays (chIP chip). Initially, polymerase chain reaction (PCR)-based DNA arrays were used for the chIP chip procedure, however, high-density oligonucleotide (HDO) arrays, which allow for the production of thousands more features per array, have emerged as a competing array platform. To compare the two platforms, data from chIP chip analysis performe  ...[more]

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