|
| Status |
Public on Mar 03, 2016 |
| Title |
RNA in fft3D |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Fft3D RNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Hu1867
genotype: h+ fft3D::hphMX ura4D18 leu1-32 ade6-216
|
| Growth protocol |
Cultures were grown at 30°C to a density of 7e6 cells/ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNA was immunoprecipitated as described earlier (Durand-Dubief, 2009) using 2µg mouse anti-myc 9E10 Sigma M4439 antibody per 100µl chromatin extracts.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled according to standard Affymetrix protocols.
|
| |
|
| Channel 2 |
| Source name |
wildtype RNA
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Hu303
genotype: h- 972
|
| Growth protocol |
Cultures were grown at 30°C to a density of 7e6 cells/ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNA was immunoprecipitated as described earlier (Durand-Dubief, 2009) using 2µg mouse anti-myc 9E10 Sigma M4439 antibody per 100µl chromatin extracts.
|
| 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.
|
| Data processing |
CEL files were normalized using quantile normalization in TAS (Affymetrix) and visualized using Podbat (www.podbat.org).
Text files contain log2 scores for enrichment over anti-myc control (for ChIP samples) and log2 scores for enrichment over wildtype RNA levels (for RNA). Tab-delimited files contain, in order: chromosome, start, end, strand, score.
|
| |
|
| Submission date |
Apr 30, 2014 |
| Last update date |
Mar 03, 2016 |
| 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 (2) |
| GSE57068 |
Role of Fun30 remodelers in retrotransposon regulation [ChIP-chip and expression analysis] |
| GSE57069 |
Role of Fun30 remodelers in retrotransposon regulation |
|
