|
| Status |
Public on Nov 01, 2010 |
| Title |
S.cerevisiae and S.paradoxus each deleted for TUP1 repeat #2 Cy5 |
| Sample type |
RNA |
| |
|
| Source name |
S. cerevisiae (BY4741 ho::kanMX4 MATa), S. paradoxus (CBS432 ho::nat1 MATα)
|
| Organisms |
Saccharomyces cerevisiae; Saccharomyces paradoxus |
| Characteristics |
organism(s): pooled sample of both species
genotype/variation: TUP1 deletion mutant
growth protocol: YPD rich medium at 30°C
|
| Growth protocol |
All samples were collected at log-phase growth. Starters were grown over night, dluted to OD(600)=0.1 in 10ml medium and harvested ~5 hours after dilution when OD(600)=~0.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using MasterPure™ Yeast RNA purification Kit (EPICENTRE).
|
| Label |
Cy5
|
| Label protocol |
Agilent Low RNA Input Amplificarion Kit (LRIAK) plus, two color p/n 5188-5340
|
| |
|
| Hybridization protocol |
Agilent Gene Expression Hybridization Kit p/n 5188-5242
|
| Scan protocol |
Arrays were scanned using Agilent Microarray Scanner (p/n G2565BA) with a 5 micron resolution and photomultiplier tube (PMT) set to 100 and then rescanned with PMT=10. The images analyzed were from the PMT=100 unless data has reached saturation. The raw images were analyzed and quantified using Spotreader software (Niles scientific).
|
| Description |
TUP1_species2
raw data file (block, dye) = TUP1.srr (block #2, Cy5)
|
| Data processing |
Raw hybridization intensities were background subtracted and log2-transformed. Results of different samples from the same condition were converted into the same distribution using percentile normalization. Probes were then sorted into 10 bins of similar %GC and the log-intensities of each bin were renormalized to the mean and Std of all probes. Finally, the normalized expression was averaged over the technical repeats of each probe (each probe was placed at 3-4 different positions on the array).
|
| |
|
| Submission date |
Aug 30, 2010 |
| Last update date |
Aug 30, 2010 |
| Contact name |
Itay Tirosh |
| E-mail(s) |
itay.tirosh@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Molecular genetics
|
| Lab |
Naama Barkai
|
| Street address |
herzl
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL8157 |
| Series (1) |
| GSE23866 |
Chromatin regulators as capacitors of inter-species expression variations |
|
