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Sample GSM4255625 Query DataSets for GSM4255625
Status Public on Jan 08, 2020
Title JHU-A53-P4
Sample type genomic
 
Channel 1
Source name Adeosquamous cancer of the pancreas
Organism Homo sapiens
Characteristics tissue source: Primary tumor
tissue type: FFPE tissue
flow sort content: Aneuploid
Growth protocol Fresh tumor samples from xenografts and patients with adenosquamous cancer of the pancreas (ASCP) were flash-frozen and maintaned at -80 degrees C. Formalin fixed paraffin embedded (FFPE) tissue samples were collected at room temperature.
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 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 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 (Ruiz, C., et al., Proc Natl Acad Sci U S A, 2011. 108(29): p. 12054-9). 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 sample type: Normal female genome
Growth protocol Fresh tumor samples from xenografts and patients with adenosquamous cancer of the pancreas (ASCP) were flash-frozen and maintaned at -80 degrees C. Formalin fixed paraffin embedded (FFPE) tissue samples were collected at room temperature.
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 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 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 (Ruiz, C., et al., Proc Natl Acad Sci U S A, 2011. 108(29): p. 12054-9). 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.
Description PancAdeSq-53-P4_21329_S01_CGH_107_Sep09_1_1
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) (Lipson et al., J Comput Biol. 2006 Mar;13(2):215-28). 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 Jan 07, 2020
Last update date Jan 08, 2020
Contact name michael thomas barrett
E-mail(s) barrett.michael@mayo.edu
Phone 480-301-6736
Organization name mayo clinic arizona
Street address 13400 east shea boulevard
City Scottsdale
State/province Arizona
ZIP/Postal code 85259
Country USA
 
Platform ID GPL19387
Series (2)
GSE143256 Genomic Landscape and Therapeutic Targets of Adenosquamous Carcinoma of the Pancreas [CGH Microarray]
GSE143565 Genomic Landscape and Therapeutic Targets of Adenosquamous Carcinoma of the Pancreas

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

Data table
ID_REF VALUE
A_16_P15000916 0.47617948
A_18_P10001325 0.6071315
A_16_P30000295 2.5230753
A_18_P10001390 0.32992306
A_18_P10001417 0.5712869
A_18_P10001440 -0.5944179
A_18_P10001457 -1.6412897
A_18_P10001486 -0.16218522
A_16_P00000027 -0.66043895
A_18_P10001545 -0.3111596
A_16_P15001543 -1.544663
A_16_P00000060 0.6819179
A_16_P15001594 2.5203505
A_16_P00000082 -0.15699399
A_16_P00000090 0.15111136
A_16_P00000099 -0.27359188
A_16_P00000104 -0.4432044
A_16_P00000113 -0.98481333
A_18_P10001772 1.3466887
A_18_P17422337 0.04419005

Total number of rows: 410786

Table truncated, full table size 10267 Kbytes.




Supplementary file Size Download File type/resource
GSM4255625_US12302336_252185021329_S01_CGH_107_Sep09_1_1.txt.gz 44.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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