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Sample GSM1096614 Query DataSets for GSM1096614
Status Public on Aug 25, 2017
Title Cirrhosis of liver CR561125
Sample type RNA
 
Source name Cirrhosis of liver
Organism Homo sapiens
Characteristics project id: 4518
facility id: 44675
sample id: CR561125
tissue: liver
gender: male
age: 71
paired: C
260/280: 2.09
260/230: 2.19
rin: 9.2
disease state: Cirrhosis of liver
Treatment protocol No treatment was involved with any of the patients.
Extracted molecule total RNA
Extraction protocol Homogenized lysate of human tissues (i.e. hepatocellular carcinoma, cirrhotic, and liver) were processed to obtain about 5 mg of high-quality total RNA using a RNeasy Midi Kit (QIAGEN, Valencia, CA, USA). The samples were obtained via tissue biorepository (OriGene Technologies, Inc., Rockville, MD, USA). The RNA integrity and quality control of 2 mL sample was assessed with NanoDrop® ND-1000 UV spectrophotometer and Agilent® 2100 Bioanalyzer at the Molecular Profiling Facility at the University of Pennsylvania. Degraded samples were eliminated from the study based on the OD A260/A280 ratios, electrophoresis results, 28S/18S rRNA ratios, and RNA Integrity Number (RIN).
Label biotin allonamide triphosphate
Label protocol Biotin Allonamide Triphosphate was used according to the standard Affymetrix protocol provided in 2012. The Ambion® WT Expression kit was used as suggested by the manufacturer to generate sense strand cDNA from 250 ng total RNA followed by fragmentation and labeling of 5.5 ug of sense strand cDNA with the GeneChip® Wt Terminal labeling kit.
 
Hybridization protocol Target hybridization was performed on Affymetrix Human GeneChip® Gene 1.0 ST Arrays (Affymetrix, Inc., Santa Clara, CA, USA) according to the manufacturer’s procedures in the GeneChip® Hybridization Oven 645, followed by washing and staining in the GeneChip® Fluidics Station 450.
Scan protocol Data acquired with GeneChip® Scanner 3000 7G (Affymetrix, Inc., Santa Clara, CA, USA)
Description Based on pathologist report of grouping stage IIIA.
Data processing The mean absolute deviation of residuals, mean absolute relative log expression, and the positive versus negative Receiver Operator Curve (ROC) Area under Curve (ROC) of the array data were metrics used to assess the overall data quality. The probe-level data (cel files) from all arrays were imported into Partek Genomics Suite software (Partek Incorporated, St. Louis, MO, USA) where RMA normalization was applied yielding log2-transformed expression intensities.
One-way ANOVA was performed on the genes across the 3 groups to provide p-values, and false positive rates were computed using the Benjamini-Hochberg step-up algorithm as implemented in Partek. Pairwise comparisons were made between tissues types providing p-values, log2 ratios, and fold-change values. Within-patient (i.e. tissues from the same human subject) log2 ratios and fold-changes were also calculated for the 3 patient sample pairs.
 
Submission date Mar 12, 2013
Last update date Aug 25, 2017
Contact name Moses Morakortoi Darpolor
E-mail(s) mdarpolor@gmail.com
Phone 2158981805
Organization name University of Pennsylvania
Department Radiology
Street address 423 Guardian Drive
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL6244
Series (1)
GSE45050 Expression data from human hepatocellular carcinoma (HCC), Cirrhosis, and non-tumor liver tissues.

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
8033433 10.5982
8052747 6.70471
7964183 9.70363
7905220 8.35129
7928330 10.0209
8097628 8.66381
7958056 8.71711
8147580 8.67472
8159086 8.70885
8114249 10.1984
8132250 7.48038
7961102 8.79982
8106418 11.9669
8079060 8.59469
8113369 7.54423
8090366 9.13228
8054439 7.57984
7922130 9.84293
7920317 11.2323
7920725 8.30021

Total number of rows: 28536

Table truncated, full table size 442 Kbytes.




Supplementary file Size Download File type/resource
GSM1096614_4518_44675_CR561125_HuGene_HuGene-1_0-st-v1_.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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