Cell cycle dependent nucleosome occupancy at cohesin binding sites in yeast chromosomes
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE8130 | GEO | 2008/03/11
SECONDARY ACCESSION(S): PRJNA101013
REPOSITORIES: GEO
Similar Datasets
Project description:Nucleosome organization determines local chromatin structure and changes in nucleosome occupancy during the cell cycle are correlated with nuclear functions. We used oligonucleotide tiling arrays to analyze the cell cycle dependence of nucleosome occupancy at cohesin binding sites in yeast chromosomes. Processed data included in Series table. Data processing: To improve the signal to noise ratio, the raw data were first processed with dCHIP with its PM/MM difference model and invariant set normalization method, using the entire dataset. 8251 out of the total 92812 probe pairs were excluded from further analysis because they either have multiple hits in the genome or the signal from the genomic hybridization was too weak (cutoff at (PM-MM)/MM < 0.25). After Gaussian smoothing (s =75 bp), the data were normalized by that of the genomic DNA. These values were then converted to log2 scale. The mean was then computed for each array. To facilitate comparisons, the different datasets were rescaled to have the same mean with log2 value of 0. The log2 ratio along the four chromosomes at all the cell cycle stages are included. The ID represents "Chromosome No_chromosomal coordinate". Keywords: time course Yeast cells were arrested at G1/S boundary with alpha factor, then released for 15 min, 40 min, 65 min and 95 min respectively. Cells were collected at each time points, then mononucleosomal DNA was purified and hybridized to Affymetrix oligonucleotide tiling arrays. Total genomic DNA was hybridized as normalization signal.
2010-05-26 | E-GEOD-8130 | biostudies-arrayexpress
Project description:Cell cycle dependent nucleosome occupancy at cohesin binding sites in yeast chromosomes
| PRJNA101013 | ENA
Project description:Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays Thirty-six ovarian tumors were profiled for copy-number alterations with the Affymetrix 100K Mapping Array. Copy number profiling of 36 ovarian tumors on Affymetrix 500K SNP arrays Sixteen ovary tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array. Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1). Affymetrix 500K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Forty-eight normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) and analyzed at the same time. One CEL file for each set (Sty and Nsp) with the median signal intensity across the set was selected as the reference array. The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows. For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set. For Chromosome X, the average of the 20 normal female samples was used. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1).
2010-12-16 | E-GEOD-26075 | biostudies-arrayexpress
Project description:In order to assess the quality of alleged PM identifications from Arabidopsis, PM-enriched fractions were compared to PM-depleted fractions using 18O isotopic labeling and mass spectrometry. The two samples submitted are biological replicates. Keywords: Protein Localization via MS Two biological replicates were analyzed in order to assess sample complexity. PM-derived vesicles were digested in 18O water and compared to PM-depleted fractions digested in 16O (natural abundance) water. Relative ion intensities were then used to calculate a heavy/lite ratio with proteins showing enrichment in the upper phase having a ratio greater than 1 or 0 on a log2 scale.
2005-06-21 | E-GEOD-2830 | biostudies-arrayexpress
Project description:The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence. Keywords: FAIRE
2006-08-11 | GSE4721 | GEO
Project description:The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence. Keywords: FAIRE
2006-08-11 | GSE4719 | GEO
Project description:The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence. Keywords: FAIRE
2006-08-11 | GSE4720 | GEO
Project description:Affymetrix GeneChip PM-MM probe pair is designed with the intension of measuring non-specific binding. Though the rationale behind the design id that a PM probe is expected to have a larger value than that of the MM probe, there are many exceptions in actual data. We gave an explanation for this inconsistency based on the assumption of functional states of a gene ‘ON/OFF’. Our hypothesis on PM-MM probe pairs is that the logarithmic of PM and MM values have the same distribution when gene is in OFF state. It means that the probability of MM > PM is expected to be equal to that of MM < PM for OFF genes. The validity of the hypothesis was given by inter-platform comparisons using common targets among three different types of platforms. Keywords: Affymetrix Gene Chip; Binomial distribution; Mathematical modeling; Oligonucleotide microarray; ON/OFF genes
2007-12-31 | GSE8353 | GEO
Project description:Background: Synchronous colorectal cancer (SCRC) is not widely studied, and one of its most striking aspects the possible clonal origin of at least a part of the cases. Materials and methods: We studied 104 paired-SCRCs of 52 consecutive patients without hereditary forms of CRC. We used a Single-Nucleotide Polymorphism array to characterize the genomic profiles, and subsequently used a statistical application to define them according to clonality within the same individual; the results were confirmed by next generation sequencing of the main CRC-related genes. We categorized the ensuing groups according to colon location, trying to find differential phenotypes with clinical implications. Results: The SCRC Monoclonal group (M) (19 cases) was divided into Monosegmental (MM) and Pancolonic (MP) groups. The MM subgroup consisted of 10 cases (19% of the total), while the MP group contained 9 cases (17%). The SCRC Polyclonal group (P) (33 cases) was also divided into Monosegmental (PM) and Pancolonic (PP) groups: 19 cases were PM (37%), showing preference for location in the left colon (17 cases, 89%), whereas 14 cases were PP (27%). Correlations with clinical features were mainly related to prognosis and familial cancer history. The MM group showed a high rate of mucinous tumors (37.5%), had the lowest mean number of tumors and associated polyps, and the worst prognosis. The MP group included the youngest age at diagnosis and the largest mean-number of associated polyps, had comparatively intermediate mean number of tumors, and showed the best prognosis and a familial cancer component. The PM group seemed to be a “frontier” group. Finally, the PP group also exhibited a mucin component, with the highest mean-number of tumors (4.6) compared with the mean-number of polyps (7.7), had a poor prognosis and consisted of sporadic cases. Conclusions: The statistical application we employed seems to define clonality more accurately in SCRC, and this, together with the tumor locations, helped us to configure a classification with prognostic and clinical value. These categories may serve as a starting point to analyze more selectively the molecular basis of SCRC and its relationship with environmental factors.
2020-01-31 | GSE110026 | GEO