|
Status |
Public on Mar 19, 2012 |
Title |
Dam-Rrp6_wt_2 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
Dam-Rrp6_wt_2
|
Organism |
Schizosaccharomyces pombe |
Characteristics |
strain: SPB437 expression: Dam-Rrp6 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 (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_wt_2
|
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 (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 |
|