|
| Status |
Public on Dec 31, 2014 |
| Title |
RNA_thp1_A |
| Sample type |
RNA |
| |
|
| Source name |
S. pombe thp1Δ
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
mating type: mating type h+
genotype: thp1Δ
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Strains were isolated from crosses and grown on YEL, no freezing of the cells prior to RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by using the hot phenol method: 20 ml of exponentially-growing cells were harvested and resuspended in 50 mM sodium acetate (pH 5.2) and 10 mM EDTA. 125 µl of 20% SDS and 1.5 ml of acidic phenol (pH 4.3) was added and the mixture was incubated for 10 min at 65°C, vigourously mixing every minute. After 5 min on ice, the supernatant was transfered to 15 ml Phase Lock Gel tubes (Lab force) to which 1.65 ml chloroform was added befor mixing by inverting the tube. The tubes were spun for 10 min at 1864 g and the supernatant was transfered to a fresh tube. The RNA was precipitated using isopropanol and resuspended in RNAse-free water.
|
| Label |
biotin
|
| Label protocol |
Samples were prepared and hybridized to Affymetrix GeneChip S. pombe Tiling 1.0FR Array according to Affymetrix specifications.
|
| |
|
| Hybridization protocol |
Samples were prepared and hybridized to Affymetrix GeneChip S. pombe Tiling 1.0FR Array according to Affymetrix specifications.
|
| Scan protocol |
The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 according to manufacturer's instruction.
|
| Description |
thp1A
|
| Data processing |
oligo-level data was rma background corrected, quantile normalized and log2 transformed using Bioconductor packages tilingArray and preprocessCore on R
log2 fold change (relative expression thp1Δ/WT was calculated by normalizing the mean of thp1_A, thp1_B and thp1_C to the mean of WT_A, WT_B and WT_C); standard deviation was calculated among WT replicates A-C and thp1Δ replicates A-C
|
| |
|
| Submission date |
Dec 30, 2014 |
| Last update date |
Jan 06, 2015 |
| Contact name |
Primo Schar |
| E-mail(s) |
primo.schaer@unibas.ch
|
| Organization name |
University of Basel
|
| Department |
Department of Biomedicine
|
| Lab |
Molecular Genetics
|
| Street address |
Mattenstrasse 28
|
| City |
Basel |
| ZIP/Postal code |
CH-4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL7715 |
| Series (1) |
| GSE64585 |
Uracil Repair - A Source of DNA Glycosylase Dependent Genome Instability |
|
