|
| Status |
Public on Mar 18, 2014 |
| Title |
ES H3K9ac ChIP replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K9ac ChIP DNA from mouse ES cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: wildtype
cell type: embryonic stem cells
strain: 129Sv-C57Bl/6
chip antibody: anti-H3K9ac (Abcam ab4441)
|
| Treatment protocol |
ChIP experiments were performed as described before (Mohn et al, Mol Cell, 2008), starting with 70 µg of chromatin and 5 µg of specific antibodies. The material was amplified using whole genome amplification kit (Sigma) before labeling for hybridization.
|
| Growth protocol |
embryonic stem cells were cultured as described previously (Bibel et al, Nat Neuroscience, 2007)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of specific antibodies. The material was amplified using whole genome amplification kit (Sigma) before labeling for hybridization.
|
| Label |
Cy5
|
| Label protocol |
According to Nimblegen standard guidelines for HD2.1 oligonucleotide tiling arrays
|
| |
|
| Channel 2 |
| Source name |
Genomic input DNA from mouse ES cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: wildtype
cell type: embryonic stem cells
strain: 129Sv-C57Bl/6
chip antibody: none (input control)
|
| Treatment protocol |
ChIP experiments were performed as described before (Mohn et al, Mol Cell, 2008), starting with 70 µg of chromatin and 5 µg of specific antibodies. The material was amplified using whole genome amplification kit (Sigma) before labeling for hybridization.
|
| Growth protocol |
embryonic stem cells were cultured as described previously (Bibel et al, Nat Neuroscience, 2007)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of specific antibodies. The material was amplified using whole genome amplification kit (Sigma) before labeling for hybridization.
|
| Label |
Cy3
|
| Label protocol |
According to Nimblegen standard guidelines for HD2.1 oligonucleotide tiling arrays
|
| |
|
| |
| Hybridization protocol |
According to Nimblegen standard guidelines for HD2.1 oligonucleotide tiling arrays
|
| Scan protocol |
According to Nimblegen standard guidelines for HD2.1 oligonucleotide tiling arrays
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction
median normalized, scaled, log2 (ChIP/Input) ratio. Calculated using the R Limma package
|
| |
|
| Submission date |
Jan 26, 2012 |
| Last update date |
Mar 19, 2014 |
| 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 |
GPL13253 |
| Series (1) |
| GSE35355 |
Acetylation at the lateral surface of the nucleosome at lysine 64 of H3 regulates chromatin dynamics and defines transcriptionally active chromatin |
|
