|
Status |
Public on Mar 18, 2014 |
Title |
ES H3K64ac ChIP replicate 1 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
H3K64ac 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-H3K64ac (Active Motif, cat. no. 39-545, lot 32908001; described in Di Cerbo et al., eLife 2014)
|
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
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|
|
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
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|
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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 |
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