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Sample GSM1205545 Query DataSets for GSM1205545
Status Public on Oct 21, 2014
Title SEQC NB patient 308
Sample type RNA
 
Source name neuroblastoma
Organism Homo sapiens
Characteristics tissue: Neuroblastoma
dataset: 2
Sex: F
age at diagnosis: 143
mycn status: 0
high risk: 0
inss stage: 4S
class label: 0
progression: 0
death from disease: 0
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]

Data table header descriptions
ID_REF
VALUE log2-transformation was applied to each normalized signal intensity value.

Data table
ID_REF VALUE
1
2
3
4
5
6
7
8
9
10
11
12 5.67
13 10.05
14 5.72
15 9.4
16 7.8
17 13.13
18 8.81
19 12.6
20 7.96

Total number of rows: 44708

Table truncated, full table size 471 Kbytes.




Supplementary file Size Download File type/resource
GSM1205545_SEQC_NB308.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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