|
| Status |
Public on Aug 06, 2013 |
| Title |
HEART_2_WCE_TAC |
| Sample type |
SRA |
| |
|
| Source name |
mouse heart
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: None
tissue: heart
treatment: TAC
genetic background: C57Bl/6J
|
| Treatment protocol |
Animals were anesthetized, intubated, then a partial thoracotomy was performed to the second rib under a surgical microscope and the sternum retracted with a chest retractor. After dissecting away thymus and fat tissue from the aortic arch the transverse aorta was identified and a small piece of 6.0 silk suture is placed between the innominate and left carotid arteries. Two loose knots are tied around the transverse aorta and a small piece of a 271/2 gauge blunt needle is placed parallel to the aorta. The first knot is tied against the needle, followed by the second knot and the needle is then removed in order to yield a constriction of approximately 0.4mm diameter. The chest retractor is removed and the rib cage closed using 6.o prolene interrupted sutures. The skin is then closed using 6.0 prolene suture with continuous pattern. The animals were treated with vehicle (DMSO) or JQ1 treatment (50 mg/kg, IP once daily) 12 hours after surgery for 4 days. Hearts were harvested 4 days after surgery
|
| Growth protocol |
Mice were grown under standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Mouse heart TAC WCE input ChIP
Barcode (already removed): ACTTGA
|
| Data processing |
Images analysis and base calling were done using the solexa pipeline.
For all samples, reads were aligned to build mm9 using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: MGSCv37
Supplementary_files_format_and_content: WIG files: For all samples, aligned sequences processed through MACS 1.4.2 and fragment pileup were outputted in .wig format.
|
| |
|
| Submission date |
Jul 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE46668 |
BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure [ChIP-Seq] |
| GSE48112 |
BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure |
|
| Relations |
| SRA |
SRX320036 |
| BioSample |
SAMN02230604 |
