|
| Status |
Public on Sep 23, 2011 |
| Title |
dcr1Δ tiling array 3 |
| Sample type |
RNA |
| |
|
| Source name |
dcr1Δ total RNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: SPB81
genotype: dcr1Δ
|
| Growth protocol |
Cells were collected at OD600=0.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using the hot phenol method (Leeds, 1991): resuspend cell pellet in 1.2 ml AE Buffer (50mM NaOAc pH 5.2, 10mM EDTA), add 80 ml 25 % SDS and 1.2 ml acidic phenol, incubate for 10 minutes at 65 °C and then put on ice for 5 minutes transfer to 15 ml phase lock Falcon tubes, add 1.3 ml chloroform, mix by inverting tube, spin 10 minutes 3000 rpm at room temperature, pour the supernatant into a 15 ml Falcon tube, add 3 ml glycogen, 4 ml 100 % ethanol and 160 ml 3M NaOAc pH 5.2-5.6, spin 30 minutes 12000 rpm at 4°C, wash 2 times with 70% ethanol, air dry pellet, resuspend in 500 ul water.
|
| Label |
biotin
|
| Label protocol |
200ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.
|
| Scan protocol |
Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.
|
| Data processing |
Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.10.0) / Bioconductor (version 2.5) package affy using the CDF environment Sp20b_M_v04.cdf (as provided in the attached file) and annotation from Netaffx (www.netaffx.com) (as provided in the attached file).
|
| |
|
| Submission date |
Jul 12, 2011 |
| Last update date |
Sep 23, 2011 |
| Contact name |
Stephan Emmerth |
| E-mail(s) |
marc.buehler@fmi.ch
|
| Organization name |
FMI
|
| Lab |
Bühler
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL10187 |
| Series (1) |
| GSE30586 |
An Extended dsRBD with a Novel Zinc-Binding Motif Mediates Nuclear Retention of Fission Yeast Dicer |
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