|
| Status |
Public on Oct 21, 2014 |
| Title |
SEQC NB patient 003 |
| Sample type |
RNA |
| |
|
| Source name |
neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Neuroblastoma
dataset: 1
Sex: F
age at diagnosis: 625
mycn status: 1
high risk: 1
inss stage: 4
class label: 1
progression: 1
death from disease: 1
|
| Treatment protocol |
All neuroblastoma samples of this set were obtained prior to any cytotoxic treatment and were snap-frozen immediately after surgery. Prior to RNA extraction tumor cell content was checked by a pathologist and only samples with >60% tumor content were processed further.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
30-60mg of snap-frozen neuroblastoma specimen was cryo-sectioned and were homogenized in TRIzol reagent (Invitrogen, Karlsruhe, Germany) using the FastPrep FP120 cell disruptor (Qbiogene, Inc, Carlsbad, CA, USA).Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent, Waldbronn, Germany). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed according to Agilent's recommentdations. In brief, 1µg total of tumor RNA was linearily amplified and labeled with Cy3 using Agilent's one-color Quick Amp Labeling Kit following the instructions of the protocol.
|
| |
|
| Hybridization protocol |
Hybridization was performed following the manufacturer's protocol. In brief, 1650 ng of Cy3-labeled cRNA was hybridized on 4x44K custom microarrays using Agilent's High-RPM Gene Expression Hyb Kit. Hybridization was performed for 17 hours at 65°C in a rotating hyb oven at 10 rpm according the company's recommendations.
|
| Scan protocol |
After washing, scanning was performed at an Agilent scanner G2505C according to the manufacturer's protocol.
|
| Data processing |
Resulting TIFF-images were processed using Agilent's Feature Extraction software Version 9.5.1.
|
| |
|
| Submission date |
Aug 09, 2013 |
| Last update date |
Oct 21, 2014 |
| Contact name |
Leming Shi |
| E-mail(s) |
lemingshi@fudan.edu.cn
|
| Phone |
+86-18616827008
|
| Organization name |
Fudan University
|
| Department |
School of Life Sciences
|
| Lab |
Center for Pharmacogenomics
|
| Street address |
2005 Songhu Road
|
| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL16876 |
| Series (2) |
| GSE47792 |
SEQC Project |
| GSE49710 |
RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [microarray] |
|
