|
| Status |
Public on Dec 31, 2007 |
| Title |
Expression analysis of human neuroblastoma (Agilent) |
| Sample type |
RNA |
| |
|
| Source name |
human neuroblastoma tissue
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue
Gender: female
Age: 13 months old
Tissue: stage III unfavorable type neuroblastoma having developed in the adrenal gland
Cells: neuroblastoma cells
|
| Biomaterial provider |
Clinical sample, Hiroshima University Hospital
|
| Treatment protocol |
At surgery, right adrenal tumor and lymph node metastasis were resected. Then, small peccieces of primary tumor was picked up and frozen immediately until use.
|
| Growth protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the frozen tissue sample by the acid-guanidium-phenol chloroform method using RNA isolation kit according to the manufacturer’s instructions (Stratagene, Agilent techonology, Santa Clara , CA), and the quality of the RNA was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent, Palo Alto, CA).
|
| Label |
Cy-3
|
| Label protocol |
The first-strand cDNA was generated from 0.5 μg of total RNA using reverse transcriptase and a T7 primer supplied in each labeling kit listed in 2-3), and then second-strand cDNA was produced using DNA polymerase mix and RNase H. cRNA (complementary RNA) was generated via an in vitro transcription reaction using T7 RNA polymerase and Cynine 3-CTP for the Agilent array. The synthesized cRNA was quantified by spectrometry and qualified using an Agilent 2100 BioanalyzerTM. The recommended amount of cRNA was then fragmented and hybridized to each array.
|
| |
|
| Hybridization protocol |
The protocol and conditions used during hybridization, blocking and washing are provided in the following source: AgilentTM Low RNA Input Fluorescent Linear Amplification Kit Protocol.
|
| Scan protocol |
The Agilent microarray was scanned using an Agilent™ DNA Microarray Scanner and processed using Agilent™ Feature Extraction software ver. 9.1.
|
| Description |
Agilent Technologies, Tokyo, Japan), were compared using the same RNA sample extracted from a human neuroblastoma tissue sample.
|
| Data processing |
Data processing Data were processed using functional ‘ON/OFF’ state of a gene.
|
| |
|
| Submission date |
Jun 30, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Eiso Hiyama |
| E-mail(s) |
eiso@hiroshima-u.ac.jp
|
| Phone |
81822575951
|
| Organization name |
Hiroshima University
|
| Department |
Natural Science Center for Basic Research and Deve
|
| Lab |
LIfe Science
|
| Street address |
1-2-3, Kasumi, Minami-ku
|
| City |
Hiroshima |
| State/province |
Hiroshima |
| ZIP/Postal code |
734-8551 |
| Country |
Japan |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE8353 |
A Mathematical Model for Affymetrix GeneChip Probe Level Data |
|
