|
| Status |
Public on Jun 30, 2022 |
| Title |
Sham 1 |
| Sample type |
SRA |
| |
|
| Source name |
skeletal muscle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: skeletal muscle
genotype: C57BL6
Sex: male
age: 16 weeks
treatment: Control
treatment time: 8 weeks
|
| Treatment protocol |
Transverse aortic constriction (TAC) was conducted on mice to induce pressure overload for cardiac hypertrophy and eventual heart failure. At 8-10 weeks post-TAC, skeletal muscle was harvest.
|
| Growth protocol |
Normal mouse chow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using miRNeasy mini kit (Qiagen Cat# 217004). 100 ng of total RNA was used for the construction of sequencing libraries.
Small RNA libraries for RNA-seq were prepared using QIAseq miRNA Library Kit (Qiagen Cat# 331505) following manufacturer's protocols.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
IDP7
|
| Data processing |
Each library was indexed in order to multiplex six samples per sequencing run on the Illumina NextSeq platform.
Primary analysis was performed using QIAseq miRNA Quantification (Qiagen software). All sample with more than 500.000 miRNA reads were analyzed.
Secundary analysis was performed using QIAseq miRNA Quantification (Qiagen software)
geNorm was used as normalization method. Fold-Change is the normalized miRNA expression in each Sample divided the normalized miRNA expression in the Control Sample.
Fold-change values less than one indicate a down-regulation, and the fold-regulation is the negative inverse of the fold-change.
For the geNorm normalization methods, the p values are calculated based on a Student's t-test of the replicate normalized miRNA expression values for each miRNA in the control group and treatment groups.
Assembly: GRCm38
Supplementary files format and content: primary analysis contains miRNA information (.xlsx)
|
| |
|
| Submission date |
Jun 28, 2022 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Samarjit Das |
| E-mail(s) |
samarjitdas@gmail.com
|
| Phone |
4432870168
|
| Organization name |
Johns Hopkins School of Medicine
|
| Department |
Anesthesiology and Critical Care Medicine
|
| Lab |
Cardiovascular
|
| Street address |
720 Rutland Avenue
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE207121 |
Contribution of skeletal muscle-specific microRNA to insulin resistance in heart failure |
|
| Relations |
| BioSample |
SAMN29402648 |
| SRA |
SRX15929955 |
