|
| Status |
Public on Jul 28, 2011 |
| Title |
Normoxic NSCLC fragments patient #1010 |
| Sample type |
RNA |
| |
|
| Source name |
Ex-vivo cultured tumor fragments from patient #1010
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Non-small cell lung cancer (NSCLC)
histology: Adenocarcinoma
treatment: Normoxia
|
| Treatment protocol |
Immediately after dissection treatment in hypoxia (1% oxygen) or normoxia (ambient oxygen) for three days
|
| Growth protocol |
Dissection of fresh NSCLC tissue into fragments app. 1mmx1mmx1mm, culture in DMEM/F12 growth medium containing 10% FCS and antibiotics in petridishes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation with Qiagen Mini kit according to manufacturer
|
| Label |
biotin
|
| Label protocol |
GeneChip® Whole Transcript (WT) Sense Target Labeling Assay; Kits : WT cDNA Synthesis and Amplification Kit 30 rxn, (Cat No. 900673); WT Terminal Labeling Kit 30rxn (Cat No. 900671)
|
| |
|
| Hybridization protocol |
GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip® fluidics station 450: protocol FS450_0007 for Cartridge Arrays
|
| Scan protocol |
Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC_3_1_1.)
|
| Description |
Gene expression data from NSCLC fragments cultured ex-vivo in ambient oxygen for three days
|
| Data processing |
Gene expression Console v.1.1, Affymetrix (Expression Console EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.4): RMA (background correction, quantile normalization accross all chips in the experiment, log2 transformation, median polish summarization)
|
| |
|
| Submission date |
Jul 27, 2011 |
| Last update date |
Jul 28, 2011 |
| Contact name |
Katharina Leithner |
| E-mail(s) |
katharina.leithner@medunigraz.at
|
| Phone |
+43 316 385 80631
|
| Organization name |
Medical University of Graz
|
| Department |
Department of Internal Medicine, Division of Pulmonology
|
| Street address |
Auenbruggerplatz 20
|
| City |
Graz |
| ZIP/Postal code |
A-8036 |
| Country |
Austria |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE30979 |
Gene expression in hypoxic non-small cell lung cancer |
|
