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Sample GSM2878359 Query DataSets for GSM2878359
Status Public on Nov 15, 2018
Title TNBC-45
Sample type genomic
 
Channel 1
Source name Resected Triple negative breast cancer
Organism Homo sapiens
Characteristics tissue: Triple negative breast cancer
pd-1/pd-l1 expression: PD-1 2/PD-L1 3 Tumor+Non tumor
grade: 3
t n: T1c N0
Growth protocol Tumor samples from patients with triple negative breast cancer were flash-frozen and maintained at -80 degrees C
Extracted molecule genomic DNA
Extraction protocol Biopsies were minced in the presence of NST buffer and DAPI according to published protocols (Holley et al, 2012). Nuclei were disaggregated then filtered through a 40 μm mesh prior to flow sorting with an Influx cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm. DNA content and cell cycle were analyzed using the software program MultiCycle (Phoenix Flow Systems, San Diego, CA).DNAs were extracted using Qiagen micro kits (Qiagen Valencia, CA).
Label Cy5
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 the smaller fragmented FFPE-derived DNA samples were digested for only 1 minute. In each case 1 ul 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 CGH arrays (Agilent Technologies, Santa Clara, CA).
 
Channel 2
Source name Reference pooled 46XX
Organism Homo sapiens
Characteristics reference: Normal female genome
Growth protocol Tumor samples from patients with triple negative breast cancer were flash-frozen and maintained at -80 degrees C
Extracted molecule genomic DNA
Extraction protocol Biopsies were minced in the presence of NST buffer and DAPI according to published protocols (Holley et al, 2012). Nuclei were disaggregated then filtered through a 40 μm mesh prior to flow sorting with an Influx cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm. DNA content and cell cycle were analyzed using the software program MultiCycle (Phoenix Flow Systems, San Diego, CA).DNAs were extracted using Qiagen micro kits (Qiagen Valencia, CA).
Label Cy3
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 the smaller fragmented FFPE-derived DNA samples were digested for only 1 minute. In each case 1 ul 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 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 10. 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.
 
Submission date Dec 06, 2017
Last update date Nov 15, 2018
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 GPL19387
Series (1)
GSE107764 The Association of Genomic Lesions and PD-1/PD-L1 Expression in Resected Triple Negative Breast Cancers

Data table header descriptions
ID_REF
VALUE Log2(Cy5/Cy3)

Data table
ID_REF VALUE
A_16_P15000916 -1.4390242
A_18_P10001325 0.5103663
A_16_P30000295 0.029198743
A_18_P10001390 -0.18622994
A_18_P10001417 0.5962877
A_18_P10001440 0.16745031
A_18_P10001457 0.51695645
A_18_P10001486 0.7831269
A_16_P00000027 0.547223
A_18_P10001545 0.5040405
A_16_P15001543 -0.73902375
A_16_P00000060 -0.09286084
A_16_P15001594 0.42634025
A_16_P00000082 -0.5923905
A_16_P00000090 -0.23724568
A_16_P00000099 -0.9702377
A_16_P00000104 -0.074962996
A_16_P00000113 -0.8000608
A_18_P10001772 -0.527078
A_18_P17422337 -0.0965366

Total number of rows: 410786

Table truncated, full table size 10468 Kbytes.




Supplementary file Size Download File type/resource
GSM2878359_US12302336_252185025155_S01_CGH_107_Sep09_1_2.txt.gz 43.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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