Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA104253 | ENA |
REPOSITORIES: ENA
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Project description:This experiment aims to map nucleosome positions and comparison of the same in WT NORMAL GROWTH vs WT-NUTRIENT STARVATION/isw1∆2∆ MUTANT/rsc4-∆4 MUTANT in Saccharomyces cerevisiae using a custom designed tiling array on Agilent plat form. The corresponding platform is submitted to GEO under Geo-ID GPL15842. 60mer probes with variable tiling density were designed for all the genes transcribed by RNA polymerase III. Each gene is tiled along with its 1kb downstream and upstream region with the exceptions of RPR1, SCR1, RDN5(1-6) and SNR52. Mononucleosomal DNA and size matched naked DNA was competitively hybridized to the array. Data was extracted and normalized log ratios were calculated using Agilent sofware. Normalized log2 ratio data was used in MLM to detection nucleosome positions.
2013-06-21 | GSE39802 | GEO
Project description:This experiment aims to map nucleosome positions and comparison of the same in WT NORMAL GROWTH vs WT-NUTRIENT STARVATION/isw1∆2∆ MUTANT/rsc4-∆4 MUTANT in Saccharomyces cerevisiae using a custom designed tiling array on Agilent plat form. The corresponding platform is submitted to GEO under Geo-ID GPL15842. 60mer probes with variable tiling density were designed for all the genes transcribed by RNA polymerase III. Each gene is tiled along with its 1kb downstream and upstream region with the exceptions of RPR1, SCR1, RDN5(1-6) and SNR52. Mononucleosomal DNA and size matched naked DNA was competitively hybridized to the array. Data was extracted and normalized log ratios were calculated using Agilent sofware. Normalized log2 ratio data was used in MLM to detection nucleosome positions. Equal amount of mono-nucleosomal DNA and sized matched naked DNA prepared from formaldehyde fixed cells (Yuan et al. 2005), was labeled with Cy5 and Cy3 respectively and hybridized to the microarray. Each Hybridization was done in triplicate from three independent biological samples in each condition. Enrichment of mono-nucleosomal DNA over naked genomic DNA is a measure of nucleosome density calculated as Log2(nucDNA/nakedDNA).
2013-06-21 | E-GEOD-39802 | biostudies-arrayexpress
Project description:Transcriptional regulation through DNA bending by Nhp6A [Agilent]
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Project description:Changes in RNA levels during osmotic stress were investigated. Total RNA was extracted from a wild-type yeast strain before and after treatment with 0.4 M NaCl and the corresponding cDNAs were hybridazed on Tiling arrays. In particular, for all the intron-containing genes, the changes in the levels of intron signal in stressed cells related to the intron signal in the non-stressed cells, and the changes in the levels of exon signal in stresses cells related to the exon signal in non-stressed cells were investigated. The supplementary bar file contains the ratios between stress signals respect to non-stress signals, using the average of the 3 biological replicas.
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