|
| Status |
Public on May 03, 2013 |
| Title |
I-Thy 113 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Thymic epithelial tumor FFPE
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Thymic epithelial tumor FFPE
who histotype: AB
age: 61.8
gender: M
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 |
|
