|
| Status |
Public on Jul 15, 2008 |
| Title |
dSSc2-FA(a) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
patient A2-forearm biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
49 yo WM, 2.5 years of dSSc
|
| Treatment protocol |
5mm punch biopsies frozen in RNAlater
|
| Growth protocol |
5mm punch biopsies frozen in RNAlater
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy for fibrous tissue
|
| Label |
Cy3
|
| Label protocol |
Agilent Low RNA Input Linear Amplification protocol: 200 ng of total RNA from each biopsy was converted to Cy3-CTP (Perkin Elmer) labeled cRNA, and Universal Human Reference (UHR) RNA (Stratagene) was converted to Cy5-CTP (Perkin Elmer) using a low input linear amplification kit (Agilent Technologies) as per manufacturers protocols. Labeled cRNA targets were then purified using RNeasy columns (Qiagen).
|
| |
|
| Channel 2 |
| Source name |
Universal Human Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
pool of RNA from 10 different human cell lines
|
| Treatment protocol |
5mm punch biopsies frozen in RNAlater
|
| Growth protocol |
5mm punch biopsies frozen in RNAlater
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy for fibrous tissue
|
| Label |
Cy5
|
| Label protocol |
Agilent Low RNA Input Linear Amplification protocol: 200 ng of total RNA from each biopsy was converted to Cy3-CTP (Perkin Elmer) labeled cRNA, and Universal Human Reference (UHR) RNA (Stratagene) was converted to Cy5-CTP (Perkin Elmer) using a low input linear amplification kit (Agilent Technologies) as per manufacturers protocols. Labeled cRNA targets were then purified using RNeasy columns (Qiagen).
|
| |
|
| |
| Hybridization protocol |
Agilent Gene Expression Hybridization kit was used for hybridization. Cy3- and Cy5-labeled cRNA was hybridized to Agilent Whole Human genome oligo-array. Hybridization was carried out for 17 hours at 65oC with rotation.
|
| Scan protocol |
Microarrays were scanned using a dual laser GenePix 4000B scanner (Axon Instruments). The pixel intensities of the acquired images were then quantified using GenePix Pro 5.0 software.
|
| Description |
NA
|
| Data processing |
Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis. Only spots with fluorescent signal at least twofold greater than local background in both Cy3- and Cy5- channels were included in the analysis. Genes missing more than 20% of their data points were excluded, resulting in 28,495 probes that passed the filtering criteria.
|
| |
|
| Submission date |
Oct 10, 2007 |
| Last update date |
Jun 13, 2017 |
| Contact name |
Tammara Wood |
| E-mail(s) |
[email protected]
|
| Organization name |
Dartmouth Medical School
|
| Department |
Biomedical Data Science
|
| Lab |
Whitfield Lab
|
| Street address |
WTRB 674
|
| City |
Lebanon |
| State/province |
NH |
| ZIP/Postal code |
03756 |
| Country |
USA |
| |
|
| Platform ID |
GPL5981 |
| Series (2) |
| GSE9285 |
Gene Expression Profiling of Scleroderma Skin |
| GSE76809 |
Multi-tissue functional genomic study of systemic sclerosis |
|
| Relations |
| Reanalyzed by |
GSE56308 |
