|
| Status |
Public on Dec 01, 2016 |
| Title |
wt_1 |
| Sample type |
RNA |
| |
|
| Source name |
wt strain
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain info.: wildtype strain
|
| Treatment protocol |
Cells were harvested and RNA extracted directly (no additional treatment).
|
| Growth protocol |
All S. pombe strains were grown in yeast extract liquid with supplements (200 mg/liter adenine; 200 mg / liter uracil; 200 mg/liter leucine) at 30oC to an absorbance of 0.5 at 600 nm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the hot phenol method [Moreno et al. (1991) Molecualr genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 194, 795-823]
|
| Label |
Biotin
|
| Label protocol |
Samples were prepared and hybridized to GeneChip® S. pombe Tiling 1.0FR (Affymetrix, Cat. No. 900647) according to Affymetrix specifications.
|
| |
|
| Hybridization protocol |
Affymetrix Gene Chip Arrays were hybridized following the "GeneChip Whole Transcript (WT) Double-Stranded Target Labeling Assay Manual" (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0002 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.
|
| Description |
S. pombe wildtype strain
|
| Data processing |
CEL files were generated with GeneChip® Command Console® Software; data preprocessing and analysis was performed in R (v3.0.1) and Bioconductor.
additional results files; Expression data for all samples as matrix (expressionDataMatrix.txt) and for each sample as a BED file.
results file descriptions: Preprocessing and analysis was performed in R (v3.0.1) and Bioconductor: The quality of the arrays was assessed with the R packages preprocessCore, oligo, affy and Starr. The R package waveTiling was used for background correction and quantile normalization. A batch effect was identified with PCA and removed using the ComBat function of the R package sva.
|
| |
|
| Submission date |
Aug 12, 2015 |
| Last update date |
Dec 01, 2016 |
| Contact name |
Ramsay Mcfarlane |
| E-mail(s) |
r.macfarlane@bangor.ac.uk
|
| Organization name |
Bangor University
|
| Department |
North West Cancer Research Institute
|
| Street address |
Brambell Building, Deiniol Road
|
| City |
Bangor |
| State/province |
Gwynedd |
| ZIP/Postal code |
LL57 2UW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL7715 |
| Series (1) |
| GSE71983 |
Differential regulation of telomere associated transcriptome homeostasis by Translin and Trax is linked to Argonaute-mediated chromosome stability control |
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