|
| Status |
Public on Aug 20, 2013 |
| Title |
New_CAG_Sham_input_rep1_l1 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Mus musculus |
| Characteristics |
tissue: heart
age: Adult
treatment: Sham
|
| Treatment protocol |
Male mice (25-30 g) were anesthetized with isofluorane blended with oxygen. The chest was shaved and cleaned with alcohol. Prior to the incision, 0.1 ml of 0.1% lidocaine was introduced under the skin. The chest cavity was opened by an incision of the left second intercostal space. The pericardial sac was opened and dissected apart, the ascending portion of aorta was dissected from the surrounding tissues and a silk suture was passed underneath the aorta and ligated against a 25- gauge needle. The needle was then removed, resulting in a ligature with a fixed diameter tied around and constricting the aorta. The sham procedure was identical except that the aorta was not ligated.
|
| Growth protocol |
All animal procedures were approved by the Institutional Animal Care and Use Committee of Boston Children’s Hospital.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fragments 150-300 bp were size-selected by 2% agarose gel electrophoresis. Recovered DNA was amplified using Phusion DNA polysome (NEB), multiplexing PCR primer 1.0, and one indexed primer. The amplified libraries were purified with Agencourt AMPure XP beads (Beckman Coulter). The libraries were quantitated using the Quant-iT DNA quantitation kit (Invitrogen). The DNA size distribution of the library was measured by an Agilent Bioanalyzer.
total cytoplasmic RNA, translating ribosome affinity purification (TRAP) RNA
2 µg of pooled input or TRAP RNA were used for two rounds of poly(A) mRNA purification by Dynabeads Oligo(dT)25 (Invitrogen). RNA was reverse transcribed by SuperScript III (Invitrogen) and random hexamer primers. After RNaseH treatment and PolI catalyzed 2nd-strand cDNA synthesis, DNA end repair was achieved by End-it kit (Epicnetre). DNA was then A-tailed with Exo- Klenow (NEB), and adaptors were ligated using Quick T4 DNA Ligase (NEB).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sham
cytoplasmic RNA
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the Ensembl NCBIM37 genome assembly using tophat version 1.4
reads were count using htseq-count version 0.5.3
Genome_build: Ensembl NCBIM37
Supplementary_files_format_and_content: RPKM
|
| |
|
| Submission date |
Jul 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Fei Gu |
| E-mail(s) |
alickgf@hotmail.com
|
| Organization name |
Childrens hospital boston, Harvard Medical School
|
| Department |
Cardiology
|
| Lab |
William Pu
|
| Street address |
320 Longwood Ave.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE45152 |
Interrogating translating RNAs and cell-type specific gene expression using Cre-activated translating ribosome affinity purification |
|
| Relations |
| BioSample |
SAMN02261547 |
| SRA |
SRX326903 |
