|
| Status |
Public on Jul 12, 2013 |
| Title |
PATIENT36 |
| Sample type |
RNA |
| |
|
| Source name |
skin biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
individual: PATIENT36
tissue: skin biopsy
gender [1 = male, 0 = female]: 0
on immunosuppressive agents [1 = yes, 0 = no]: 0
race: Caucasian
age: 58
antibody group: None
fvc predicted: 95
fvc less than 70: No ILD
total skin score: 2
dlco predicted: 103
|
| Treatment protocol |
The samples were put immediately in RNALater (Qiagen).
|
| Growth protocol |
A 3mm punch skin biopsy was obtained from the arm of study subjects.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We extracted total RNA utilizing RNeasy Fibrous Tissue (Qiagen) according to manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Using the Ambion Illumina TotalPrep RNA Amplification kit (Ambion #IL1791), we reverse-transcribed 300 ng of total RNA using a T7 oligo-dT primer, used the resulting cDNA to synthesize the complement strand, purified, and in vitro transcribed biotinylated cRNA.
|
| |
|
| Hybridization protocol |
We incubated the cRNA with HYB buffer with the BeadChips at 58C for 17 hours and washed according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide.
|
| Scan protocol |
We incubated each BeadChip with Cy3-Streptavidin for 10 min, dried, and then scanned on an Illumina BeadArray Scanner.
|
| Description |
PATIENT36
Total RNA hybridized onto an Illumina HT-12 v4.0 gene expression microarray.
|
| Data processing |
The raw data were exported from Illumina GenomeStudio (no background subtraction was performed). The data were log2 transformed and normalized by quantiles using BRB-Array Tools.
|
| |
|
| Submission date |
May 21, 2013 |
| Last update date |
Jun 22, 2021 |
| Contact name |
Jeffrey Chang |
| E-mail(s) |
jeffrey.t.chang@uth.tmc.edu
|
| Organization name |
University of Texas
|
| Street address |
6431 Fannin St
|
| City |
Houston |
| ZIP/Postal code |
77019 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE47162 |
Skin gene expression correlates of severity of interstitial lung disease in systemic sclerosis |
| GSE58095 |
Dissecting the heterogeneity of skin gene expression patterns in systemic sclerosis. |
|
