|
| Status |
Public on Jul 30, 2018 |
| Title |
H3K27ac ChIP-seq TAC operation (Week 1) |
| Sample type |
SRA |
| |
|
| Source name |
Cardiomyocytes
|
| Organism |
Mus musculus |
| Characteristics |
operation: TAC operation (Week 1)
histone modification: H3K27ac
strain: C57BL/6
|
| Treatment protocol |
Mice (8 weeks old) underwent transverse aortic constriction (TAC) to induce heart failure. The transverse aorta was constricted with a 7-0 silk suture paralleled with a 27-gauge blunt needle, which was removed after constriction. Transthoracic echocardiography was performed on conscious mice with a Vevo 2100 imaging system (VisualSonics). M-mode echocardiographic images were obtained from a longitudinal view to measure left ventricular size and function and were used to assess whether the heart was appropriately exposed to pressure overload.
|
| Growth protocol |
C57BL/6 mice were purchased from CLEA JAPAN. All mice were maintained in specific pathogen-free conditions in the animal facilities of the University of Tokyo. All animal experiments were approved by Ethics Committee for Animal Experiments of the University of Tokyo and strictly adhered to the animal experiment guidelines. Male mice at 8 weeks of age were used for all experiments.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cardiomyocytes (1,000,000 cells) were isolated from two mice 1 week after the TAC operation with Langendorff perfusion, were crosslinked with 1% formaldehyde at room temperature for 10 min and were quenched with 0.125 M glycine. After sonication, soluble chromatin was added with 4 μl recombinant histone 2B (New England Biolabs) and 0.5 μl of mouse RNA (Qiagen) and was incubated with the antibody-bead complex (5 μg of anti-H3K27ac antibody (Abcam, ab4729) and 20 μl of Dynabeads Protein G (Thermo Fisher Scientific, 10003D)) at 4 °C overnight. Immunoprecipitates were washed, reverse-crosslinked and incubated with proteinase K and RNase A. DNA was purified using a MinElute PCR Purification Kit (QIAGEN).
Sequencing libraries were prepared using the TruSeq Kit (Illumina) for high-throughput sequencing on an Illumina HiSeq 2500 according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were mapped to the mouse genome (mm9) using Bowtie (version 1.1.1) with the parameters ‘-S -m 1 -l 36 -n 2 mm9’.
RPKM was calculated with reads mapped to the nuclear genome using DEGseq (version 1.8.0).
ChIP-seq peaks were identified with the MACS program version 1.3.7.1 with a P value < 1e-5. The other parameters were as follows: --tsize ‘36’, --gsize ‘1865500000’, --mfold ‘10’, --nomodel, --nolambda, --wig.
Sequence reads aligning to the region were extended by 300 bp and the density of reads in each region was normalized to the total number of million mapped reads for producing the normalized read density in units of reads per million mapped reads (RPM).
Genome_build: mm9
Supplementary_files_format_and_content: Normalized ChIP-seq counts (bigWig file) and ChIP-seq peak calls (BED file) were generated using the MACS program.
|
| |
|
| Submission date |
Feb 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Seitaro Nomura |
| E-mail(s) |
senomura-cib@umin.ac.jp
|
| Phone |
81338155411
|
| Organization name |
The University of Tokyo
|
| Department |
Department of Cardiovascular Medicine
|
| Street address |
7-3-1, Hongo, Bunkyo-ku
|
| City |
Tokyo |
| State/province |
Select a State or Province |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE95142 |
Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure (ChIP-Seq) |
| GSE95143 |
Cardiomyocyte stress-response gene modules regulate cardiac hypertrophy and failure |
|
| Relations |
| BioSample |
SAMN06352676 |
| SRA |
SRX2580936 |
