|
Status |
Public on Feb 26, 2016 |
Title |
Fresh frozen intrahepatic bile duct biopsy 18 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
Intrahepatic cholangiocarcinoma
|
Organism |
Homo sapiens |
Characteristics |
gender: female tissue type: Intrahepatic cholangiocarcinoma (ICC)
|
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: female 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 ICC18
|
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 |
|