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Sample GSM391288 Query DataSets for GSM391288
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

Data table header descriptions
ID_REF
VALUE dChip (2008) PM only signal intensity
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
7892501 3.37 P
7892502 2.07 P
7892503 4.96 P
7892504 26.67 P
7892505 6.44 P
7892506 2.31 P
7892507 12.56 P
7892508 4.32 P
7892509 84.71 P
7892510 6.88 P
7892511 2.85 P
7892512 20.86 P
7892513 4.01 P
7892514 41.11 P
7892515 32.17 P
7892516 3.81 P
7892517 10.08 P
7892518 3.24 P
7892519 2.91 P
7892520 156.64 P

Total number of rows: 33252

Table truncated, full table size 502 Kbytes.




Supplementary file Size Download File type/resource
GSM391288.CEL.gz 5.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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