Illumina HiSeq 2000 sequencing; Identification of CaMKII-dependent H3S28p target genes
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Cardiovascular
Cell type
Heart
MeSH Description
The hollow, muscular organ that maintains the circulation of the blood.
Attributes by original data submitter
Sample
ENA first public
2019-06-13
ENA last update
2019-06-03
ENA-CHECKLIST
ERC000011
External Id
SAMEA5684516
INSDC center alias
Institute of Experimental Cardiology, University of Heidelberg, Heidelberg, Germany; and DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
INSDC center name
Institute of Experimental Cardiology, University of Heidelberg, Heidelberg, Germany; and DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Germany
INSDC first public
2019-06-13T04:03:25Z
INSDC last update
2019-06-03T12:50:10Z
INSDC status
public
Submitter Id
E-MTAB-8011:H3S28P CamkII DKO 2
age
8
broker name
ArrayExpress
common name
house mouse
developmental stage
adult
genotype
CaMKII and CaMKII double knockout
individual
mixed pool of 3 hearts
organism part
heart
sample name
E-MTAB-8011:H3S28P CamkII DKO 2
sex
male
strain
C57BL/6N
Sequenced DNA Library
library_name
H3S28P CamkII DKO 2_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Mouse hearts are perfused in a Langendorff apparatus and digested via liberase solution (Roche), the cells are going through different Ca2+ containing solutions. Cells are subcequently plated in a cellculture dish. The cells get fixated via incubation of 1% formaldehyde for 10 min at RT. The reaction is quenced using Glycin at a final concentration of 250 mM. Finally, the cells get collected and centrifuged to a cell pellet. The cells are lysed with the following buffers: Buffer1: 50mM Hepes‐KOH pH7.5, 140 mM NaCl, 1mM EDTA, 0.2ml 10% glycerol, 0.5% NP‐40, 0.25% Triton, X‐100 Buffer2: 200mM NaCl, 1mM EDTA (pH 8), 0.5mM EGTA (pH 8), 10mM Tris (pH 8) Buffer3: 50mM Tris (pH 8), 0,1% SDS, 0,95 % NP40, 0,1% Na-deoxycholate, 10mM EDTA, 150mM NaCl. The chromatin is fragmented via bioruptor sonification (Diagenode) using 4x10 cycles of sonification. The dna is precipitated using phenol/chloroform/isoamylalcohol and PhaseLock Tubes (5prime). Libraries are prepared according to the manufacture's protocol (NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina)