|
| Status |
Public on Mar 02, 2015 |
| Title |
Cnd2 ChIP in wt |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
wt Cnd2-GFP anti-GFP ChIP
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Hu2413
genotype/variation: cnd2-GFP::NatR
molecule subtype: immunoprecipitated DNA
|
| Treatment protocol |
For ChIP experiments, DNA was immunoprecipitated as described earlier (Durand-Dubief, 2009) using 2µl of anti-H4K12Ac (ab1761, abcam, Lot: 920722), 2µl of anti-myc (9E10, sigma), 1 µl of anti-GFP (ab290, abcam, Lot: GR76757-1), or 3µl anti-RNA polymerase II CTD repeat (ab5408, abcam, Lot: GR32519-1) antibodies per 100µl chromatin extracts.
|
| Growth protocol |
Cultures were grown at 30°C to a density of 7e6 cells/ml.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted as described in Moreno et al., Methods Enzym. 1991. ChIP was carried out as described in Durand-Dubief et al., Methods Mol Biol, 2009.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled according to standard Affymetrix protocols.
|
| |
|
| Channel 2 |
| Source name |
anti-GFP ChIP in wt
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Hu0029
genotype/variation: h- ade6-M210 leu1-32 ura4-D18
molecule subtype: immunoprecipitated DNA
|
| Treatment protocol |
For ChIP experiments, DNA was immunoprecipitated as described earlier (Durand-Dubief, 2009) using 2µl of anti-H4K12Ac (ab1761, abcam, Lot: 920722), 2µl of anti-myc (9E10, sigma), 1 µl of anti-GFP (ab290, abcam, Lot: GR76757-1), or 3µl anti-RNA polymerase II CTD repeat (ab5408, abcam, Lot: GR32519-1) antibodies per 100µl chromatin extracts.
|
| Growth protocol |
Cultures were grown at 30°C to a density of 7e6 cells/ml.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted as described in Moreno et al., Methods Enzym. 1991. ChIP was carried out as described in Durand-Dubief et al., Methods Mol Biol, 2009.
|
| 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 |
Ch1 CEL files: cnd2_anti-GFP_1.CEL; cnd2_anti-GFP_2.CEL
Ch2 CEL files; wt_anti-GFP_1.CEL; wt_anti-GFP_2.CEL
Cnd2_wt_ChIP
|
| 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. DamID/ChIP sample CEL-files were normalised together with their Dam Control/mock 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. For DamID, tiling array probe scores were averaged over DpnI/II restriction fragments.
Tab-delimited txt-files contain probe positions and log2 scores for all probes used in this analysis.
Please note that DamID data table contains 29698 data rows. DamID is a method that uses methylation-specific restriction enzymes for the selection of targets. The resolution of DamID is therefore limited to the distance between these restriction sites. When we processed the data, we averaged tiling array probe scores over each restriction fragment. This results in fewer data points, and therefore smaller tables [Steglich et al., Nucleus (2012) or Greil et al., Methods Enzym. (2006)].
|
| |
|
| Submission date |
May 29, 2013 |
| Last update date |
Mar 03, 2015 |
| 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) |
| GSE47464 |
Role of Fft3 in nuclear organization [DamID-chip, ChIP-chip] |
| GSE58013 |
Role of Fft3 in nuclear organization |
|
