|
| Status |
Public on Oct 29, 2022 |
| Title |
Cre negative rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Left Ventricle
|
| Organism |
Mus musculus |
| Characteristics |
time point: 4 days post injury
age: 6 to 10 weeks
cre: Negative
injury type: Left anterior artery ligation
parental lines: Jackson Laboratory stocks 027929, 029645, and 030532
|
| Treatment protocol |
Permenant ligation of the left anterior descending artery was conducted to produce a surgical myocardial infarction. Mice were administered tamoxifen citrate diet ad libitum immediately after surgery to promote excession of myofibroblast Yap and Wwtr1. Left ventricles were collected 4 days post injury.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Left ventricles of mice taken 4 days after surgery were homogenized in TRIzol. RNA was subsequently collected and purified by phenol/chloroform extraction. RNA quality was determined using an Agilent BioAnalyzer.
RNA libraries were prepared by BGI Americas
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Sequencing was performed using a DNBSEQ-G400 platform at 20M, 100bp pair-end reads per sample.
Reads were filtered using SOAPnuke (v1.5.2) removing reads with adaptors and unknown bases > 0.1%.
Bowtie2 (v2.2.5) was used to map reads to the GRCm38.p6
Expression data was generated using RSEM (v1.2.12)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Spread sheets include FPKM values for each Sample and expression data for each experimental group
|
| |
|
| Submission date |
Dec 21, 2020 |
| Last update date |
Oct 29, 2022 |
| Contact name |
Michael Andrew Flinn |
| Organization name |
Medical College of Wisconsin
|
| Department |
Physiology
|
| Lab |
O'Meara Lab
|
| Street address |
8701 W Watertown Plank Rd
|
| City |
Wauwatosa |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL28457 |
| Series (2) |
| GSE163612 |
RNA-seq of injured mouse hearts depleted for myofibroblast Yap and Wwtr1 |
| GSE163617 |
RNA-seq of injured mouse hearts depleted for myofibroblast Yap or Yap and Wwtr1 |
|
| Relations |
| BioSample |
SAMN17128066 |
| SRA |
SRX9710372 |
