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ABSTRACT:
PROVIDER: PRJNA109717 | ENA |
REPOSITORIES: ENA
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Project description:Background Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization behavior of various degrees of mismatch (MM) structure has not been extensively studied. Here, we present the results of two large-scale microarray experiments on S.cerevisiae and H.sapiens genomic DNA, to explore MM oligonucleotide behavior with real sample mixtures under tiling-array conditions. Results We examined all possible nucleotide substitutions at the central position of 36-nucleotide probes, and found that nonspecific binding by MM oligos depends upon the individual nucleotide substitutions they incorporate: C->A, C->G and T->A (yielding purine-purine mispairs) are most disruptive, whereas A->X were least disruptive. We also quantify a marked GC skew effect: substitutions raising probe GC content exhibit higher intensity (and vice versa). This skew is small in highly-expressed regions (±0.5% of total intensity range) and large (±2% or more) elsewhere. Multiple mismatches per oligo are largely additive in effect: each MM added in a distributed fashion causes an additional 21% intensity drop relative to PM, three-fold more disruptive than adding adjacent mispairs (7% drop per MM). This SuperSeries is composed of the following subset Series: GSE13172: Mismatch oligonucleotides in human GSE13174: Mismatch oligonucleotides in yeast Refer to individual Series
2010-05-05 | E-GEOD-13175 | biostudies-arrayexpress
Project description:Tiled regions surrounding 5 human genes as 36mers, HBG2, TIMP3, SYN3, FLNA, FBX07. The first three of these genes, we tiled with various mismatch oligos in addition to 'perfect match' oligos. Keywords: Mismatch hybridization experiment Tiled perfect match and various designs of mismatch oligonucleotide for several human genes. Goal was to observe the influence of various MM types on hybridization behavior in human, and compare it to yeast (see related slide).
2010-05-05 | E-GEOD-13172 | biostudies-arrayexpress
Project description:Tiled 10kb region centered around ACT1 gene (YFL039C, CHROMOSOME 6 @ coords 48760-59195), double-stranded, 36mers at 1bp spacing, with mismatches and deletions; also tiled 6 genes of interest (YBL092W, YGR155W, YOL040C, YOR312C, YMR242C, YLR229C), coding strand only, 36mers at 1bp spacing, with some mismatches and deletions Keywords: Mismatch hybridization experiment Tiled perfect match and various designs of mismatch oligonucleotide for several yeast genes. Goal was to observe the influence of various MM types on hybridization behavior in yeast and compare it to human (see related slide).
2010-05-05 | E-GEOD-13174 | biostudies-arrayexpress
Project description:Mutation accumulation in mismatch repair deficient yeast
| PRJNA209500 | ENA
Project description:This study aimed to model formamide-based melting for the optimization of the sensitivity and specifcity of oligonucleotide probes in dignostic high-density microarrays. Formamide melting profiles of DNA oligonucleotides were obtained with a high-density microarray targeting 16S rRNA genes of Escherichia coli and Rhodobacter sphaeroides. One or two mismatched versions of perfect match probes were included on the array to systematically analyze the effect of formamide on mismatch stability and mismatch discrimination. A thermodynamics-based mathematical model of formamide denaturation was developed to predict the formamide melting profiles with sufficient accuracy to help with oligonucleotide design in microbial ecology applications.
2012-06-30 | GSE33021 | GEO
Project description:The experiments are done with three libraries by introducing base-pair perturbations on Widom 601: (1) poly(dA:dT) tract library (2) mismatch library (3) insertion library. And additional two more libraries based on native yeast genomic sequences: (4) Park97 mismatch library (5) Park97 insertion library. And we measured the nucleosome positioining in the base-pair resolution for before and after sliding by Chd1 chromatin remodeler.
2022-05-12 | GSE198440 | GEO
Project description:Tiled regions surrounding 5 human genes as 36mers, HBG2, TIMP3, SYN3, FLNA, FBX07. The first three of these genes, we tiled with various mismatch oligos in addition to 'perfect match' oligos. Keywords: Mismatch hybridization experiment
2009-02-18 | GSE13172 | GEO
Project description:Expansion of triplex-forming GAA/TTC repeats in the first intron of FRDA gene is known to cause Friedreich’s ataxia. Besides FRDA, there are a number of other highly polymorphic GAA/TTC loci in the human genome where the size variations so far were considered to be a neutral event. Using yeast as a model system, we demonstrate that expanded GAA/TTC repeats represent a threat to eukaryotic genome integrity by triggering double-strand breaks and gross chromosomal rearrangements. The fragility potential strongly depends on the length of the track and orientation of the repeats relative to the replication origin which correlates with their propensity to adopt secondary structure and to block replication progression. We show that fragility is mediated by mismatch repair machinery and requires the MutS(beta) and endonuclease activity of MutL(alpha). We suggest that the mechanism of GAA/TTC-induced chromosome aberrations defined in yeast can also operate in human carriers with expanded tracks. Keywords: CGH-array
2008-05-14 | GSE11425 | GEO