|
| Status |
Public on Mar 12, 2019 |
| Title |
Control4 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Male
age: 19
group: Control
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A miRNeasy Mini Kit (Qiagen, Cat:217004) was used to isolate the RNA following the manufacturer's guidelines
A Illumina TruSeq kit was used in library preparation following the manufacturer's guidelines.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Control4
|
| Data processing |
Data was mapped to the mouse geneome using TopHat2 and the UCSC mm10 mouse genome as reference.
Gene expression was quantified using Cufflinks 2 and the Genecode reference.
Differential gene expression was determined using EdgeR.
Supplementary_files_format_and_content: xlsx file contains the cpm for the Samples and the calculated log2ratio for the KO samples compared to the NTG samples along with the FDR and pvalue for the comparison.
|
| |
|
| Submission date |
Oct 04, 2018 |
| Last update date |
Mar 12, 2019 |
| Contact name |
AJ Marian |
| E-mail(s) |
Ali.J.Marian@uth.tmc.edu
|
| Phone |
7134476700
|
| Organization name |
The University of Texas Health Science Center Houston
|
| Department |
Institute of Molecular Medicine
|
| Lab |
Cardiovascular Genetics
|
| Street address |
3742 Arnold St
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77005 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE120836 |
Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes is Associated with Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy [RNA-Seq] |
| GSE120838 |
Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes is Associated with Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy |
|
| Relations |
| BioSample |
SAMN10176590 |
| SRA |
SRX4797387 |
