|
| Status |
Public on Jun 12, 2012 |
| Title |
Cid14_wt_1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Dam-Cid14_wt_1
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: SPB436
expression: Dam-Cid14
genotype/variation: wt
|
| Treatment protocol |
Harvested cells were spheroplasted to remove cell wall
|
| Growth protocol |
Strains grown at 30 degress in YES medium to OD600=0.4
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA isolated using Dneasy Blood and Tissue Kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
The DNA was fragmented and labeled using the Affymetrix GeneChip® GeneChip Hybridization, Wash, and Stain Kit according to the manufactuer's instructions
|
| |
|
| Channel 2 |
| Source name |
Dam_only_wt_1
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: SPB435
expression: Dam only
genotype/variation: wt
|
| Treatment protocol |
Harvested cells were spheroplasted to remove cell wall
|
| Growth protocol |
Strains grown at 30 degress in YES medium to OD600=0.4
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA isolated using Dneasy Blood and Tissue Kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
The DNA was fragmented and labeled using the Affymetrix GeneChip® GeneChip Hybridization, Wash, and Stain Kit according to the manufactuer's instructions
|
| |
|
| |
| Hybridization protocol |
hybridization was performed for 16h at 45°C and 60rpm in an Affymetrix hybridization oven; washing steps were done in an Affymetrix Fluidics station with the Affymetrix protocol FS450_0002
|
| Scan protocol |
GeneChips were scanned with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.
|
| Data processing |
Oligo-level data was rma background corrected, quantile normalized and log2 transformed using Bioconductor packages tilingArray and preprocessCore on R. Contrasts were computed on the oligo level by subtracting respective columns of expression. Differential expression values for individual features in the file sPombegenomicelementsV02_ALL.txt were calculated by averaging enrichment values for all the oligos overlapping the individual features, considering only features covered by at least 50 oligos. This produces the DamID_results.txt file [contains all 8014 features for which DamID enrichment was calculated, with a separate column for each of the 4 contrasts].
Results files linked as supplementary files on Series record.
|
| |
|
| Submission date |
Mar 30, 2012 |
| Last update date |
Jun 13, 2012 |
| Contact name |
Katrina Woolcock |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Lab |
Bühler
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL7715 |
| Series (1) |
| GSE36956 |
DamID for Cid14 in wild-type and swi6∆ |
|
