|
| Status |
Public on Aug 26, 2016 |
| Title |
Patient 004, baseline |
| Sample type |
RNA |
| |
|
| Source name |
PAH-SSc patient_baseline
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: 004
patient condition: pulmonary arterial hypertension and scleroderma (PAH-SSc)
timepoint: 0 weeks; baseline
clinical outcome: positive
tissue: whole blood
|
| Treatment protocol |
Each subject received Tadalafil at 40mg once daily dose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood samples collected before treatment with Tadalafil and 16 weeks post-treatment were collected using PaxGene Tubes. RNA samples were prepared from frozen whole blood samples using the QIAGEN Rneasy kit (QIAGEN, Valencia, CA). Sample integrity was verified using RNA 6000 Pico Assay RNA Chips and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).
|
| Description |
Baseline 4
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1) and an Entrez Gene-specific probeset mapping (version 14.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan.
|
| |
|
| Submission date |
Nov 18, 2015 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL15034 |
| Series (1) |
| GSE75173 |
Changes in Gene Expression Profiles in Patients with Pulmonary Arterial Hypertension Associated with Scleroderma Treated with Tadalafil |
|
