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Sample GSM2561880 Query DataSets for GSM2561880
Status Public on Oct 02, 2017
Title Sample I
Sample type genomic
 
Channel 1
Source name Probe_I
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

Data table header descriptions
ID_REF
VALUE normalized LogRatio (Log10 (rProcessedSignal/gProcessedSignal))

Data table
ID_REF VALUE
1 9.05E-02
2 -2.37E-01
3 -2.27E-01
4 -6.79E-02
5 1.10E-01
6 -7.57E-02
7 -3.81E-02
8 6.04E-02
9 3.11E-02
10 3.20E-02
11 -3.21E-03
12 2.98E-02
13 -9.32E-02
14 -3.54E-02
15 -6.05E-02
16 7.35E-02
17 -8.32E-02
18 1.93E-02
19 -1.29E-01
20 3.33E-02

Total number of rows: 420288

Table truncated, full table size 6670 Kbytes.




Supplementary file Size Download File type/resource
GSM2561880_IRB_19_Cy3_Biopsie_1_Chernobyl_Pat_Cy5_12878_1_2.txt.gz 43.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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