Natural variation of histone modification and its impact on gene expression in rat
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
2012-05-30T17:00:31Z
ENA-LAST-UPDATE
2018-03-08T15:46:29Z
External Id
SAMEA1325184
INSDC center name
Max-Delbrueck-Center, MDC, Berlin
INSDC first public
2012-05-30T17:00:31Z
INSDC last update
2018-03-08T15:46:29Z
INSDC status
public
StrainOrLine
BXH09
Submitter Id
E-MTAB-1102:lv-H3K4me3-BXH09-male-bio1-tech1.bam
age
6 week
broker name
ArrayExpress
common name
Norway rat
developmental stage
adult
organism part
heart
sample name
E-MTAB-1102:lv-H3K4me3-BXH09-male-bio1-tech1.bam
scientific_name
Rattus norvegicus
Sequenced DNA Library
library_name
DNA_Extract_lv-H3K4me3-BXH09-male-bio1-tech1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Rats were kept in the animal facility of the Institute of Physiology, Czech Academy of Science (Prague, Czech Republic) in a climate-controlled environment with 12h light/dark cycles. Rats were housed in polystyrene cages containing wood shavings and fed standard rodent chow and water ad libitum. Six weeks old male rats were sacrificed by cervical dislocation and tissue (left ventricle of the heart and liver) was collected between 8 and 10 am, snap frozen in liquid nitrogen and stored at -80 C. All animal procedures were in accordance with the Animal Protection Law of the Czech Republic. ChIP samples were prepared as previously described (Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-37, 2007) with following changes: Frozen LV and liver tissue was crunched using pestle and mortar. 125mg tissue was homogenized in a Potter- Elvehjem tissue grinder, nuclei were isolated and digested with MNase (Sigma- Aldrich) to generate native chromatin templates consisting mainly of mononucleosomes. Chromatin was precipitated with anti-H3K4me3 (NEB, 9751 S), anti-H3K27me3 (Millipore, 07-449), anti-H3K4me1 (Abcam, ab8895), or anti- H4K20me1 (Abcam, ab9051) and antibody-bound DNA fragments were purified by MinElute PCR Purification Kit (QIAGEN). Specificity of immunoprecipitation was confirmed with known genes by qPCR. 50ng of DNA was used for construction of ChIP-seq libraries according to the manufacturer's protocol (Illumina/Solexa).