|
| Status |
Public on Jan 18, 2012 |
| Title |
Man1_DamID |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Man1 DamID gDNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Hu2130
|
| Growth protocol |
Cultures were grown at 30°C to a density of 7x10^6 cells/ml.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted as described in Moreno et al., Methods Enzym. 1991.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled according to standard Affymetrix protocols.
|
| |
|
| Channel 2 |
| Source name |
DamCtrl DamID
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Hu2078
|
| Growth protocol |
Cultures were grown at 30°C to a density of 7x106 cells/ml.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted as described in Moreno et al., Methods Enzym. 1991.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled according to standard Affymetrix protocols.
|
| |
|
| |
| Hybridization protocol |
Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.
|
| Scan protocol |
Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.
|
| Description |
supplementary_file_descriptions: Tab-delimited txt-files contain probe positions and log2 scores for all probes used in this analysis.
|
| Data processing |
CEL.files were analysed in R (http://www.r-project.org) using the Bioconductor (http://www. bioconductor.org) packages “affy”, “affxparser” and “preprocessCore” with standard parameters. Ima1/Heh2-DamID sample CEL-files were normalised together with their Dam Control sample CEL-files using quantile normalization with standard parameters. Probe sequences were mapped to the S.pombe genome draft downloaded from ftp://ftp.sanger.ac.uk/ on Nov 19, 2009. Any probes mapping to more than one location in the genome or mapping with more than one mismatch was excluded from further analysis.
|
| |
|
| Submission date |
Jul 07, 2011 |
| Last update date |
Jan 18, 2012 |
| Contact name |
Babett Steglich |
| Organization name |
Universitätsklinikum Hamburg-Eppendorf
|
| Street address |
Martinistrasse 52
|
| City |
Hamburg |
| ZIP/Postal code |
20246 |
| Country |
Germany |
| |
|
| Platform ID |
GPL7715 |
| Series (1) |
| GSE30476 |
DamID of Ima1 and Man1 in Schizosaccharomyces pombe |
|
