|
| Status |
Public on Jun 01, 2014 |
| Title |
S288C-2 (reanalysis of GSM786821) |
| Sample type |
genomic |
| |
|
| Source name |
reference strain
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: S288C
|
| Treatment protocol |
no treatment (CGH)
|
| Growth protocol |
overnight YPD shaken culture 28°
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction according to legras et al. 2003 FEMS microbiol letters.
|
| Label |
biotin
|
| Label protocol |
winzeler2003Genetics
|
| |
|
| Hybridization protocol |
Winzeler2003 Genetics
|
| Scan protocol |
Affymetrix scanner
|
| Description |
GSM786821
|
| Data processing |
Background substraction with RMA and quantile normalisation and perfect match probe extraction with "apt-1-12-0" (241710 probes)
Then probes are filtered for having coordinates on S288C genome sequence (Schizosacchaomyces pombe probes are removed), probes are scaled across all arrays. Probes with signal values below 5 for one of S288C array or aberant values over 10000 3 probes on the whole dataset) are removed. 38864 probes are left.
From the filtered data, for each probe, after averaging the signal from replicates , the log ratios otained on are calculated using S288C as a reference . NA values are repalced by -2 hybridization on S288C genome and negative or null for other srains mean no hybridization of the probe)
The average of log ratios are calculated for three adjacent positions in order to group them three by three in order to reduce the number of probes (too many probes lead to a crash of DNAcopy). Log ratios are then centered by substracting the median value.
Discontinuities in hybridization signal are detected with DNAcopy R package.
results file descriptions: RMA-bg quantile intensity file (RMAbackground quantile normalisation-probe intensity file)
results file descriptions: RMA-bgquantil+Saccerecoordinates (RMAbackground quantile normalisation-probe intensity file of Saccharomyces cerevisiae probes + coordinates)
results file descriptions: Log ratios for each probe (chromosome numbering changed from Sace A to 1 as requested by DNAcopy)
results file descriptions: Log ratios after averaging per three probes and centered
results file descriptions: Eg8segments (segments of hybridization found with DNAcopy for Eg8_
results file descriptions: CECT11758segments (segments of hybridization found with DNAcopy for CECT11758)
results file descriptions: Eg25segments (segments of hybridization found with DNAcopy for Eg25)
results file descriptions: FloraNerosegments (segments of hybridization found with DNAcopy for Flora Nero)
results file descriptions: LRJurasegments (segments of hybridization found with DNAcopy for LR Jura)
results file descriptions: MY138segments (segments of hybridization found with DNAcopy for My138)
results file descriptions: P3segments (segments of hybridization found with DNAcopy for P3)
results file descriptions: TA12CUBsegments (segments of hybridization found with DNAcopy for TA12CUB)
results file descriptions: U13segments (segments of hybridization found with DNAcopy for U13)
results file descriptions: V5segments (segments of hybridization found with DNAcopy for V5)
|
| |
|
| Submission date |
Mar 14, 2014 |
| Last update date |
Jun 01, 2014 |
| Contact name |
Jean-Luc Legras |
| E-mail(s) |
[email protected]
|
| Organization name |
INRA
|
| Department |
UMR1083, Science pour l'Oenologie
|
| Lab |
Equipe Microbiologie - Physiologie Integrative
|
| Street address |
2, place Viala
|
| City |
Montpellier cedex1 |
| ZIP/Postal code |
34060 |
| Country |
France |
| |
|
| Platform ID |
GPL2529 |
| Series (1) |
| GSE55925 |
Population Structure and Comparative Genome Hybridization of European flor yeast reveal a unique group of Saccharomyces cerevisiae strains with few gene duplications in their genome |
|
| Relations |
| Reanalysis of |
GSM786821 |
