Mus musculus
Protocols: Cells were fixed with 1% formaldehyde for 8 min at room temperature. Nuclei were isolated using Lysis Buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40), transferred to Sonication Buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM EGTA, 4 mM EDTA, 0.1% SDS, 1% Triton X-100, 1% NP-40) and sonicated (Bioruptor, Diagenode) for 2 cycles of 30 sec on / 30 sec off, for 15 min at high intensity. Each immunoprecipitation (IP) was carried out on the equivalent of 50 x 106 cells in IP Buffer (150 mM NaCl, 50 mM Tris-HCl pH 7.5, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100) overnight at 4°C. The antibody slurry was prepared with 50 µl A-, 50 µl G-Dynabeads and 60 µg.ml-1 antibody per IP. Immunoprecipitated chromatin was treated with RNaseA and the DNA isolated using 2% Na SDS and 2mg.ml-1 Proteinase-K. Two or more biological replicates were analyzed for each antibody. ChIP DNA samples were quality controlled by qPCR before being sent for library preparation and 50 base single-end sequencing on an Illumina HiSeq 2000 (McGill University and Génome Québec Innovation Centre).
ENA first public
2017-07-08
ENA last update
2017-07-07
External Id
SAMEA104156230
INSDC center alias
UZH
INSDC center name
University of Zurich
INSDC first public
2017-07-08T17:04:14Z
INSDC last update
2017-07-07T18:20:20Z
INSDC status
public
Submitter Id
E-MTAB-5839:ChIP-seq_UBF_MEFs_Rrn3fl_Rep2
broker name
ArrayExpress
cell type
mouse embryonic fibroblast
common name
house mouse
genotype
Rrn3fl/fl ERCre+/+ p53-/-
sample name
E-MTAB-5839:ChIP-seq_UBF_MEFs_Rrn3fl_Rep2