|
| Status |
Public on Oct 05, 2021 |
| Title |
P_40 |
| Sample type |
RNA |
| |
|
| Source name |
HEMB
|
| Organism |
Homo sapiens |
| Characteristics |
condition: DCM with LV systolic dysfunction (LVEF < 45 percent) and symptoms of HF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Column based RNA extraction (Qiagen) was performed following the manufacturers instructions for total RNA isolation from fibrous tissues, including purifications step using Charge Switch Total RNA Cell Kit. RNA integrity was checked using RNA 6000 Pico LabChip on a Bioanalyzer 2100 (Agilent)
|
| Label |
biotin
|
| Label protocol |
Two round T7 RNA polymerase mediated linear amplification was performed with 14-25ng RNA starting amount according to the Affymetrix manufacturers Two Cycle Target Labelling protocol
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip System Confocal Scanner 3000.
|
| Description |
patient
|
| Data processing |
Expression raw data were transferred to Rosetta Resolver 7.2 (Rosetta Inpharmatics LLC) and Rosetta extraction algorithm was performed. For further analyses probe sets exhibiting p<0.05 were used. The pipeline calculates expression summaries using MAS5 via Affymetrix Power Tools from scans using both the perfect-match (PM) and mis-match (MM) probes. It returns only sequence-level results. The resulting P-values may be used as a guideline to decide expression presence or absence. This pipeline combines the expression values for individual profiles using an arithmetic average and computes the error of the result. P-value is the geometric mean of the profile-level P-values. Results are computed from sequence-level data using group processing. All profiles in the experiment definition are normalized together.
|
| |
|
| Submission date |
Oct 05, 2018 |
| Last update date |
Oct 05, 2021 |
| Contact name |
Sabine Ameling |
| Organization name |
Universitätsmedizin Greifswald
|
| Department |
Interfakultäres Institut für Genetik und Funktionelle Genomforschung
|
| Lab |
Funktionelle Genomforschung
|
| Street address |
Jahnstraße 15a
|
| City |
Greifswald |
| ZIP/Postal code |
17487 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE120895 |
Correlation of clinical parameters of heart failure with myocardial gene expression in dilated cardiomyopathy |
|
