|
| Status |
Public on Jun 22, 2017 |
| Title |
Dam.mst2pdp3D_spb2212.1 |
| Sample type |
genomic |
| |
|
| Source name |
Dam fused to Mst2 in pdp3D cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
expression: Dam-Mst2
genotype: pdp3D
strain number: spb2212
|
| Treatment protocol |
Harvested cells were spheroplasted to remove cell wall
|
| Growth protocol |
Cells were grown to early exponential phase (OD=0.4) and harvested.
|
| 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.
|
| Description |
data column in DamID_results.txt file: Dam.mst2pdp3D_spb2212.1_vs_Damonly_492.1
|
| 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].
All results file are summarised in DamID_results.txt file
DamID_results.txt is a table containing all 17910 features for which DamID enrichment was calculated with a separate column for each of the 14 contrasts
|
| |
|
| Submission date |
Jan 11, 2017 |
| Last update date |
Jun 22, 2017 |
| Contact name |
Fabio Mohn |
| E-mail(s) |
fabio.mohn@fmi.ch
|
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Lab |
Buehler Lab
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL7715 |
| Series (2) |
| GSE93433 |
The histone acetyltransferase Mst2 prevents epigenetic silencing via specific acetylation of the ubiquitin ligase Brl1 [microarray data] |
| GSE93434 |
The histone acetyltransferase Mst2 prevents epigenetic silencing via specific acetylation of the ubiquitin ligase Brl1 |
|
