|
| Status |
Public on Aug 06, 2011 |
| Title |
deltaOfd2_normoxia_90min |
| Sample type |
RNA |
| |
|
| Source name |
S. pombe delta-Ofd2 (SPAP8A3.02c), normoxia, 90 min
|
| Organism |
Schizosaccharomyces pombe 972h- |
| Characteristics |
genotype/variation: deletion strain Ofd2 (SPAP8A3.02c)
|
| Treatment protocol |
For hypoxia growth conditions (<1% oxygen) cells were cultured for 90 minutes in the AnaeroGen system (Oxoid), as per the manufacturer’s instructions. For normoxia (20% oxygen) cells were grown in conical flasks exposed to normal room level oxygen conditions.
|
| Growth protocol |
Strains were grown at 30˚C with shaking to exponential phase (OD=0.5) in yeast extract media containing 2% glucose (YES) plus supplements (225µg/ml each of histidine, leucine, adenine, lysine and uracil)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested at 4˚C and total RNA was isolated and purified using the RNeasy Mini Kit (Qiagen) in-conjunction with the RNase-Free DNase Set (Qiagen) to remove genomic DNA as per manufacturer’s instructions.
|
| Label |
cy3
|
| Label protocol |
Labeling was performed by Roche NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by Roche NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by Roche NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is deletion strain of Ofd2 grown under normal oxygen conditions
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Aug 05, 2011 |
| Last update date |
Aug 06, 2011 |
| Contact name |
David Lando |
| E-mail(s) |
dl280@cam.ac.uk
|
| Organization name |
Cambridge University
|
| Department |
Gurdon Institute
|
| Lab |
Tony Kouzarides
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10720 |
| Series (1) |
|
