|
| Status |
Public on Oct 02, 2017 |
| Title |
Sample 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Probe_1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: basal cell carcinoma
|
| Growth protocol |
samples were mechanically grinded in liquid nitrogen; we added a digestion step with 1 µg RNAse A at 37°C for 30 minutes, samples were washed in 200µl 1xTE-buffer
controls (suspension cells) were washed in PBS twice and centrifuged at 6000g. Afterward controls were treated same as samples
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from tissue samples with Quiagen Genomic DNA Isolation Kit Mini for Blood and Tissue (Version 04/12).
|
| Label |
Cy3
|
| Label protocol |
Samples were labeled with Cy3 and reference DNA (GM12878) was labeled Cy5 according to manufactures protocol (Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells, or Tissues, ProtocolVersion 7.3 March 2014).
|
| |
|
| Channel 2 |
| Source name |
GM12878_0Gy_0h_IV
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
tag: IV
|
| Growth protocol |
samples were mechanically grinded in liquid nitrogen; we added a digestion step with 1 µg RNAse A at 37°C for 30 minutes, samples were washed in 200µl 1xTE-buffer
controls (suspension cells) were washed in PBS twice and centrifuged at 6000g. Afterward controls were treated same as samples
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from tissue samples with Quiagen Genomic DNA Isolation Kit Mini for Blood and Tissue (Version 04/12).
|
| Label |
Cy5
|
| Label protocol |
Samples were labeled with Cy3 and reference DNA (GM12878) was labeled Cy5 according to manufactures protocol (Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic Labeling for Blood, Cells, or Tissues, ProtocolVersion 7.3 March 2014).
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized on a whole genome array (Agilent®, Santa Clara, CA, USA; SurePrint G3 Human Genome CGH Microarray 2x400K, 5.3 kb spacing).
|
| Scan protocol |
Agilent® Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 7.3 March 2014; Agilent® G2505C; Scan Control Version A.8.1.3; resolution 3 µm; 16 bit TIFF; no XDR; Images were quantified using Agilent Feature Extraction Software (version 12.0).
|
| Data processing |
Agilent Feature Extraction Software (v 12.0) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Apr 03, 2017 |
| Last update date |
Oct 02, 2017 |
| Contact name |
Benjamin Becker |
| E-mail(s) |
benjamin3becker@bundeswehr.org
|
| Organization name |
Bundeswehr Institute for Radiobiology
|
| Department |
Genomics II
|
| Street address |
Neuherbergstr. 11
|
| City |
Munich |
| ZIP/Postal code |
80804 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9777 |
| Series (1) |
| GSE97334 |
CNA analysis of ionizing radiation related basal cell carcinoma |
|
