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Sample GSM4255612 Query DataSets for GSM4255612
Status Public on Jan 08, 2020
Title PAX208-F2-P4
Sample type genomic
 
Channel 1
Source name Adeosquamous cancer of the pancreas
Organism Homo sapiens
Characteristics tissue source: Patient derived xenograft
tissue type: frozen tissue
flow sort content: human tumor and mouse host
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 PAX208F2-AR-P4_27822_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 1.9562423
A_18_P10001325 0.53473634
A_16_P30000295 1.7606838
A_18_P10001390 1.5439799
A_18_P10001417 0.22527412
A_18_P10001440 0.07331948
A_18_P10001457 0.18599638
A_18_P10001486 1.8369803
A_16_P00000027 0.29961565
A_18_P10001545 0.67483246
A_16_P15001543 0.831436
A_16_P00000060 1.6053997
A_16_P15001594 0.45653224
A_16_P00000082 0.91117144
A_16_P00000090 2.2819524
A_16_P00000099 0.4364115
A_16_P00000104 0.13843054
A_16_P00000113 1.2374042
A_18_P10001772 0.4525082
A_18_P17422337 0.7171774

Total number of rows: 410786

Table truncated, full table size 10348 Kbytes.




Supplementary file Size Download File type/resource
GSM4255612_US12302336_252185027822_S01_CGH_107_Sep09_1_1.txt.gz 43.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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