|
| Status |
Public on Mar 04, 2010 |
| Title |
Unruptured, Rep5 |
| Sample type |
RNA |
| |
|
| Source name |
Full-thickness vessel wall sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Full-thickness vessel wall sample
type: Unruptured
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Specimens were homogenized with a rotor-stator homogenizer in buffer RLT. Next, total RNA was isolated using RNeasy Fibrous Tissue Minikit (Qiagen) according to the manufacturer’s protocol and treated with DNase I (Qiagen). RNA concentration was determined by product absorbance at 260 nm measured by NanoDrop ND-1000 (NanoDrop Technologies, Montchanin, DE). The quality of RNA was additionally assessed using RNA 6000 Nano LabChip Kit and Agilent Bioanalyzer 2100 (Agilent, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
A starting amount of 1μg of high-quality total RNA was used for rRNA reduction. mRNA (rRNA reduced) was converted to double-stranded cDNA and further to cRNA using GeneChip® WT Sense Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA). The procedure consists of double-stranded cDNA synthesis, cRNA amplification, second cycle of cDNA synthesis and fragmentation of the single-stranded DNA. Each sample was synthesized from an independent biological sample. The fragmented single-stranded DNA was subsequently labeled using recombinant terminal deoxynucleotidyl transferase (TdT).
|
| |
|
| Hybridization protocol |
Labeled cDNA was hybridized to an Affymetrix GeneChip Human Gene ST 1.0 array (Affymetrix) at 45oC for 17 hours as recommended by the manufacturer. These arrays contain 764,885 probes representing 28,869 well-annotated genes. Arrays were washed and stained in Fluidic Station 450 (Affymetrix) according to manufacturer’s standard protocol.
|
| Scan protocol |
The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA).
|
| Description |
Unruptured, Replicate 5, Gender unknown
|
| Data processing |
Data was normalized by dChip 2008 (quantile normalization, PM only)
|
| |
|
| Submission date |
Apr 10, 2009 |
| Last update date |
Mar 04, 2010 |
| Contact name |
Marcin Piechota |
| E-mail(s) |
marpiech@if-pan.krakow.pl
|
| Phone |
(+4812) 6623328
|
| Organization name |
Institute of Pharmacology PAS
|
| Department |
Molecular Neuropharmacology
|
| Street address |
Smetna 12
|
| City |
Krakow |
| ZIP/Postal code |
31-343 |
| Country |
Poland |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE15629 |
Global expression profiling of ruptured and unruptured human intracranial aneurysms |
|
