|
| Status |
Public on Feb 26, 2016 |
| Title |
Fresh frozen extrahepatic bile duct biopsy 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Extrahepatic cholangiocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
tissue type: Extrahepatic cholangiocarcinoma (ECC)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
AllPrep DNA/RNA Mini kit (Qiagen)
|
| Label |
Alexa flour 5
|
| Label protocol |
BioPrime Total Genomic DNA Labeling System (Invitrogen)
|
| |
|
| Channel 2 |
| Source name |
matched normal
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
sample type: normal control (reference)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
AllPrep DNA/RNA Mini kit (Qiagen)
|
| Label |
Alexa flour 3
|
| Label protocol |
BioPrime Total Genomic DNA Labeling System (Invitrogen)
|
| |
|
| |
| Hybridization protocol |
Agilent ChIP-on-chip protocol v9
|
| Scan protocol |
DNA Microarray scanner (Agilent, no G2565CA); Feature Extraction Software 10.5 (Agilent) and the standard ChIP protocol (Agilent)
|
| Description |
ductal adenocarcinoma
ECC1
|
| Data processing |
Feature extracted data was processed using the R statistical environment, version 2.13. (http://www.R-project.org) and bioconductor. Background correction and log2-ratio (M-value, test/reference) transformation were performed according to the NormExp method with offset=50 correction methods for two-color microarrays. To reduce variations between co-hybridized samples, intensity-based LOESS normalization on rank-invariant probes and negative controls was applied.
|
| |
|
| Submission date |
Mar 07, 2013 |
| Last update date |
Feb 27, 2016 |
| Contact name |
Dieter Weichenhan |
| E-mail(s) |
d.weichenhan@dkfz.de
|
| Organization name |
DKFZ Heidelberg
|
| Department |
C010 Epigenomics
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
D-69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9767 |
| Series (1) |
| GSE44965 |
Human cholangiocarcinoma (CC), ECC (extrahepatic CC) and ICC (intrahepatic CC) cases versus control |
|
