|
| Status |
Public on Mar 19, 2012 |
| Title |
Dam-Dcr1_normal |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Dam-Dcr1_normal
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: SPB381
expression: Dam-Dcr1
treatment: normal
|
| Treatment protocol |
Harvested cells were spheroplasted to remove cell wall
|
| Growth protocol |
Strains grown at 30 degress in YES medium to OD600=0.4 (unless otherwise stated)
|
| 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_normal
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: SPB492
expression: Dam_only
treatment: normal
|
| Treatment protocol |
Harvested cells were spheroplasted to remove cell wall
|
| Growth protocol |
Strains grown at 30 degress in YES medium to OD600=0.4 (unless otherwise stated)
|
| 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
additional results files: DamID_results.tab
results file descriptions: DamID_results.tab is a table containing all 8014 features for which DamID enrichment was calculated with a separate column for each of the 64 contrasts.
|
| |
|
| Submission date |
Feb 29, 2012 |
| Last update date |
Mar 19, 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 (2) |
| GSE36167 |
DamID for Swi6, Rdp1, Dcr1, Ago1, Arb1, Cid14, Rrp6, Nup85 and Amo1 in Schizosaccharomyces pombe |
| GSE36214 |
RNA interference keeps Atf1-bound stress response genes in check at nuclear pores |
|
