NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1480328 Query DataSets for GSM1480328
Status Public on Aug 17, 2014
Title benign_PCPG_1 [aCGH]
Sample type mixed
 
Channel 1
Source name benign_PCPG
Organism Homo sapiens
Characteristics subject gender: M
subject age (yrs): 51
diagnosis: paraganglioma (PGL)
tissue: pheochromocytoma/paraganglioma (PCPG)
primary site: retroperitoneum
tissue type: benign
Extracted molecule genomic DNA
Extraction protocol Array CGH was performed using the Agilent Human whole genome CGH 60 K microarray.1.5 g of test DNA and reference DNAs was digested with Alu I and Rsa I (Promega, Madison, WI) and purified using the QIAprep Spin Miniprep kit (Qiagen, Germantown, MD).
Label Cy3
Label protocol Test DNA and reference DNA samples were labelled by random priming with either Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS.
 
Channel 2
Source name reference DNA
Organism Homo sapiens
Characteristics sample type: reference DNA (Promega human genomic DNA male G1471)
Extracted molecule genomic DNA
Extraction protocol Array CGH was performed using the Agilent Human whole genome CGH 60 K microarray.1.5 g of test DNA and reference DNAs was digested with Alu I and Rsa I (Promega, Madison, WI) and purified using the QIAprep Spin Miniprep kit (Qiagen, Germantown, MD).
Label Cy3
Label protocol Test DNA and reference DNA samples were labelled by random priming with either Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS.
 
 
Hybridization protocol After labelling, the individual samples and reference samples were combined and concentrated using Microcon YM-30 filters (Millipore, Billerica, MA). After probe denaturation and preannealing with Cot-1 DNA, hybridisation was performed at 65°C with rotation for 40 hours. Four washing steps were completed with Agilent Oligo CGH washes as follows: Wash Buffer 1 at room temperature for 5 min, Wash Buffer 2 at 37°C for 1 min, an acetonitrile rinse at room temperature for 1 min, and a 30-second wash at room temperature in Agilent’s Stabilization and Drying Solution.
Scan protocol All slides were scanned on an Agilent DNA microarray scanner G2505C.
Data processing Raw log2 ratio was normalized using qunatile normalizaion provided by limma package (http://bioconductor.org).
 
Submission date Aug 16, 2014
Last update date Aug 17, 2014
Contact name Yoon-La Choi
E-mail(s) yla.choi@samsung.com
Organization name Samsung medical center
Department Department of pathology
Lab Laboratory of cancer genomics and molecular pathology
Street address 81 Irwon-Ro, Gangnam-gu
City Seoul
ZIP/Postal code 135-710
Country South Korea
 
Platform ID GPL10152
Series (2)
GSE60457 Copy number profiles of pheochromocytoma and paraganglioma
GSE60459 Expression and copy number profiles of pheochromocytoma and paraganglioma

Data table header descriptions
ID_REF
VALUE normalized Log2 ratio (test/reference)

Data table
ID_REF VALUE
1 -0.038001991
2 0.026575595
3 0.026575595
4 0.515001713
5 -0.344961525
6 -0.100768268
7 -0.504047424
8 0.290363507
9 0.282878082
10 -0.027956849
11 0.216523503
12 0.198580789
13 0.093586406
14 0.52918106
15 -0.155719378
16 0.216104236
17 0.623836301
18 -0.039786693
19 0.091910247
20 0.163421606

Total number of rows: 62976

Table truncated, full table size 1120 Kbytes.




Supplementary file Size Download File type/resource
GSM1480328_US10123791_252800414328_1_1.txt.gz 6.5 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap