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Sample GSM577176 Query DataSets for GSM577176
Status Public on May 03, 2013
Title I-Thy 049
Sample type genomic
 
Channel 1
Source name Thymic epithelial tumor FFPE
Organism Homo sapiens
Characteristics tissue: Thymic epithelial tumor FFPE
who histotype: B3
age: 45.4
gender: F
labeling kit: ULS labeling kit
Growth protocol All cell lines were cultured in RPMI 1640 containing 200 mM L-Glutamine (Gibco, Invitrogen, Grand Island, NY), 50 U/mL penicillin, 50 U/mL streptomycin (Invitrogen) and 10% heat-inactivated calf serum (Invitrogen) and grown in a 37 oC incubator with humidified 5% CO2 atmosphere. Media was supplemented with 25nM Hepes for T1889 and T1682.
Extracted molecule genomic DNA
Extraction protocol FFPE tumor specimens were assessed for quality and adequacy of fixation and storage. A Hematoxylin & Eosin stained slide was prepared for each sample. A pathologist verified the presence of tumor tissue and marked the areas with more than 80% cancer cells on the paraffin blocks. Five cores of tissue were punched from the marked area on FFPE blocks using a 0.6-mm tissue microarray needle, to a depth of approximately 1 mm. The DNA was extracted using DNeasy kit (Qiagen, Inc., Valencia, CA) according to Genomic DNA ULS labeling kit protocol (Agilent Technologies, Inc., Palo Alto, CA)
Label Cy5
Label protocol The labeling procedure was conducted using the Genomic DNA Enzymatic Labeling Kit (Agilent) for 7 samples and using the Genomic DNA ULS labeling kit (Agilent) for the remaining 52 samples
 
Channel 2
Source name Promega Genomic DNA
Organism Homo sapiens
Characteristics sex: Male
labeling kit: ULS labeling kit
Growth protocol All cell lines were cultured in RPMI 1640 containing 200 mM L-Glutamine (Gibco, Invitrogen, Grand Island, NY), 50 U/mL penicillin, 50 U/mL streptomycin (Invitrogen) and 10% heat-inactivated calf serum (Invitrogen) and grown in a 37 oC incubator with humidified 5% CO2 atmosphere. Media was supplemented with 25nM Hepes for T1889 and T1682.
Extracted molecule genomic DNA
Extraction protocol FFPE tumor specimens were assessed for quality and adequacy of fixation and storage. A Hematoxylin & Eosin stained slide was prepared for each sample. A pathologist verified the presence of tumor tissue and marked the areas with more than 80% cancer cells on the paraffin blocks. Five cores of tissue were punched from the marked area on FFPE blocks using a 0.6-mm tissue microarray needle, to a depth of approximately 1 mm. The DNA was extracted using DNeasy kit (Qiagen, Inc., Valencia, CA) according to Genomic DNA ULS labeling kit protocol (Agilent Technologies, Inc., Palo Alto, CA)
Label Cy3
Label protocol The labeling procedure was conducted using the Genomic DNA Enzymatic Labeling Kit (Agilent) for 7 samples and using the Genomic DNA ULS labeling kit (Agilent) for the remaining 52 samples
 
 
Hybridization protocol According to ULS labeling kit protocol version 3 November 2008
Scan protocol According to ULS labeling kit protocol version 3 November 2008
Description Thymic epithelial tumor FFPE
Platform GPL4093 is based on NCBI Build 35, and Platform GPL10123 is based on NCBI Build 36.
Data processing Data were extracted and normalized using the linear method by Feature Extraction v10.5 (Agilent).
Copy number call thresholds were defined: high gain +0.8, gain +0.3, loss -0.3 and big loss -0.8
Data were further Centralized. For complete details, please see readme.txt supplementary file on the Series record. Centralized data files are available as Sample supplementary files.
 
Submission date Aug 10, 2010
Last update date May 03, 2013
Contact name Iacopo Petrini
E-mail(s) i.petrini@sssup.it
Phone 00393428566432
Organization name Pisa University
Street address Via Roma 67
City Pisa
ZIP/Postal code 56100
Country Italy
 
Platform ID GPL10123
Series (1)
GSE23540 Copy number aberrations of genes regulating normal thymus development in thymic epithelial tumors

Data table header descriptions
ID_REF
VALUE normalized signal intensity

Data table
ID_REF VALUE
1 7.94E-02
2 0.00E+00
3 0.00E+00
4 0.00E+00
5 0.00E+00
6 0.00E+00
7 5.92E-01
8 0.00E+00
9 0.00E+00
10 0.00E+00
11 0.00E+00
12 0.00E+00
13 -8.12E-02
14 0.00E+00
15 0.00E+00
16 0.00E+00
17 0.00E+00
18 0.00E+00
19 0.00E+00
20 0.00E+00

Total number of rows: 180880

Table truncated, full table size 2803 Kbytes.




Supplementary file Size Download File type/resource
GSM577176_US82400122_252206010742_S01_CGH_105_Dec08_1_4.txt.gz 18.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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