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Sample GSM1586552 Query DataSets for GSM1586552
Status Public on Dec 23, 2017
Title Tumor, Splenic Diffuse Red Pulp Lymphoma, case 4
Sample type genomic
 
Channel 1
Source name Tumor, Splenic Diffuse Red Pulp Lymphoma, case 4
Organism Homo sapiens
Characteristics cell type: splenic diffuse red pulp lymphoma
gender: male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted form formalin fixed paraffin embedded (FFPE) tissues by phenol chloroform method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.
Label Cy5
Label protocol Following manufacturer instructions (Agilent)
 
Channel 2
Source name pool normal DNA
Organism Homo sapiens
Characteristics gender: M
age: 20
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted form formalin fixed paraffin embedded (FFPE) tissues by phenol chloroform method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.
Label Cy3
Label protocol Following manufacturer instructions (Agilent)
 
 
Hybridization protocol The protocol Oligonucleotide Array-Based CGH for Genomic DNA Analysis (ULS labeling for Blood, Cells, Tissues or FFPE) was used.
Scan protocol Scanned on an Agilent G2565AA scanner.
Description Tumor vs normal
Data processing Raw data were generated from scanned images using Agilent Feature Extraction Software (10.10.1.1). Log2ratios of background corrected values for tumour over normal DNA were calculated. Normalization was carried out on Agilent's CGH Analytics, integrated on the Agilent Genomic Workbench Standard Edition 6.5.0.58, using data from the internal set of control probes included in the microarray. Detection of Copy Number Alterations (CNAs) was performed using the ADM-2 algorithm, also implemented within the Agilent's genomics suite Genomic Workbench v5.0, with a threshold of 6.5 and a minimum of 5 consecutive probes and Nexus 6.0 Discovery Edition (Biodiscovery, El segundo, CA).
 
Submission date Jan 16, 2015
Last update date Dec 23, 2017
Contact name Alba Navarro
E-mail(s) ANAVARRL@clinic.ub.es
Organization name IDIBAPS - Hospital ClĂ­nic
Department Pathology
Lab Molecular Pathology
Street address Villaroel, 170
City Barcelona
ZIP/Postal code 08036
Country Spain
 
Platform ID GPL8736
Series (2)
GSE64822 Clinical and molecular characterization of splenic diffuse red pulp lymphomas
GSE65060 Clinical and molecular characterization of splenic diffuse red pulp lymphomas [Agilent]

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
1 -0.009098482402
2 0
3 0.4232551427
4 0.01743068967
5 0.4679417659
6 -0.09469980176
7 -0.1222076963
8 0.2905322869
9 0.05923212326
10 -0.1379265399
11 -0.01280570299
12 -0.001609045201
13 -0.1986142522
14 -0.1336370766
15 0.02108974252
16 -0.01339164516
17 0.1385244001
18 0.03301871093
19 0.05588914116
20 -0.273589595

Total number of rows: 974016

Table truncated, full table size 19710 Kbytes.




Supplementary file Size Download File type/resource
GSM1586552_Case_4.txt.gz 269.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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