|
| Status |
Public on Oct 08, 2014 |
| Title |
BY4742, biological rep. 2 |
| Sample type |
RNA |
| |
|
| Source name |
Total RNA from BY4742 cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
genotype: MATa his3∆1 leu2∆0 lys2∆0 ura3∆0
|
| Growth protocol |
Each strain was grown to mid-log phase in liquid YPD medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the Rneasy Midi kit (QIAGEN)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix.
|
| Scan protocol |
Microarrays were scanned using GeneChip® Scanner 3000 7G
|
| Description |
Gene expression data from mid-log yeast cells in YPD medium
|
| Data processing |
Normalization was performed using the dChip application software (http://www.dchip.org). All arrays were normalized together with those of W301-A, hpr1∆, tho2∆, and sub2∆, published in Gomez-Gonzalez et al., 2011 (accesion number GSE24802). Previous to normalization, a mask file from Affymetrix (s_cerevisiae.msk) was applied to exclude S.pombe probes. Normalization was performed with PM probes (invariant set normalization and model-based expression) and the outliers treated as missing data in the subsequent analyses. For each strain, the expression profile was compared with its isogenic wild type and the genes showing at least a 1.5-fold expression change considered as altered (parameters: absolute difference between signal in mutant versus wild type >100; difference P-value <0.05). Genes with model-based expression values below 600 (the median expression value of meiotic genes in our experiments) in at least 50% of the samples were removed before the comparisons to reduce the false positives.
|
| |
|
| Submission date |
Apr 10, 2014 |
| Last update date |
Oct 08, 2014 |
| Contact name |
Andrés Aguilera |
| Organization name |
CABIMER, Universidad de Sevilla
|
| Department |
Genome BIology
|
| Lab |
Genome Instability & Cancer
|
| Street address |
Av. Américo Vespucio 24
|
| City |
Seville |
| ZIP/Postal code |
41092 |
| Country |
Spain |
| |
|
| Platform ID |
GPL2529 |
| Series (2) |
| GSE56702 |
Expression data from Saccharomyces cerevisiae strains deleted for the THSC/TREX-2 subunits Thp1, Sac3 and Sus1 |
| GSE56703 |
Microarray and ChIP-chip analyses of the THSC/TREX-2 complex |
|
