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Sample GSM8302703 Query DataSets for GSM8302703
Status Public on Sep 24, 2024
Title High grade serous ovarian carcinoma FF1
Sample type genomic
 
Channel 1
Source name Surgical resection
Organism Homo sapiens
Characteristics tissue source: Resection
tissue type: frozen tissue
flow sort content: Human tumor
t n: Tumor
Growth protocol Fresh tumor samples were flash-frozen and maintained at -80 degrees C.
Extracted molecule genomic DNA
Extraction protocol Frozen tissue samples were minced in the presence of NST buffer and DAPI according to published protocols. Nuclei from each sample were disaggregated then filtered through a 40 μm mesh prior to flow sorting with an Aria III cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm.
Label Cy-3
Label protocol DNAs from frozen tissue were treated with DNAse 1 prior to Klenow-based labeling. High molecular weight templates were digested for 30 minutes while DNAs. In each case 1 µl of 10x DNase 1 reaction buffer and 2 μl of DNase 1 dilution buffer were added to 7 μl of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols (22). All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to 400k CGH arrays (Agilent Technologies, Santa Clara, CA)
 
Channel 2
Source name Reference pooled 46XX
Organism Homo sapiens
Characteristics sample type: Normal female genome
Growth protocol Fresh tumor samples were flash-frozen and maintained at -80 degrees C.
Extracted molecule genomic DNA
Extraction protocol Frozen tissue samples were minced in the presence of NST buffer and DAPI according to published protocols. Nuclei from each sample were disaggregated then filtered through a 40 μm mesh prior to flow sorting with an Aria III cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm.
Label Cy-5
Label protocol DNAs from frozen tissue were treated with DNAse 1 prior to Klenow-based labeling. High molecular weight templates were digested for 30 minutes while DNAs. In each case 1 µl of 10x DNase 1 reaction buffer and 2 μl of DNase 1 dilution buffer were added to 7 μl of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols (22). All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to 400k CGH arrays (Agilent Technologies, Santa Clara, CA)
 
 
Hybridization protocol Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol for 40 hours in a rotating 65°C oven.
Scan protocol All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 11.0 using default settings.
Data processing Data was extracted from the TIFF files using Agilent FE 11. The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm (ADM2)[23]. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval, and to the square root of the number of probes in the interval.
Log2(Cy5/Cy3)
 
Submission date Jun 03, 2024
Last update date Sep 24, 2024
Contact name Michael Thomas Barrett
E-mail(s) barrett.michael@mayo.edu
Phone 480-301-6736
Organization name Mayo Clinic Arizona
Department Molecular Pharmacology and Experimental Therapeutics
Street address 13400 East Shea Boulevard
City Scottsdale
State/province AZ
ZIP/Postal code 85259
Country USA
 
Platform ID GPL9777
Series (1)
GSE268921 Single Nucleus DNA Sequencing of Flow Sorted Archived Frozen and Formalin Fixed Paraffin Embedded Solid Tumors

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 1.576613903e-002
2 0.000000000e+000
3 0.000000000e+000
4 3.117323340e-002
5 -1.461518456e-001
6 -2.293872702e-002
7 -3.847152582e-002
8 1.646943613e-001
9 4.589780469e-002
10 1.802631862e-001
11 1.199738154e-001
12 -1.451558216e-001
13 -1.747634460e-001
14 -4.882080224e-003
15 8.731282538e-002
16 4.606963872e-002
17 -1.507153489e-001
18 -1.387730826e-001
19 -6.714112380e-003
20 2.938811210e-002

Total number of rows: 420288

Table truncated, full table size 9964 Kbytes.




Supplementary file Size Download File type/resource
GSM8302703_US90200265_252185035706_S01_CGH_1201_Sep17_1_2.txt.gz 43.0 Mb (ftp)(http) TXT

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