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Sample GSM299096 Query DataSets for GSM299096
Status Public on Sep 05, 2008
Title human cultured bladder HB DM, subject 12
Sample type RNA
 
Source name human
Organism Homo sapiens
Characteristics Female, age 57
Disease status: HB (control (stress incontinence, no bladder pain))
Culture medium: DM (differentiating medium)
Treatment protocol A single cold-cup bladder biopsy was taken and transported immediately to the laboratory in growth medium. Each biopsy was divided into 6-10 pieces using fine scissors and optical loupes. The pieces were distributed into a 6-well plate with 1-2 pieces per well. 1.5 ml growth medium was added to each well and the plate was incubated at 37oC, 5% carbon dioxide. Additional medium was added to the wells on day 3, and a schedule of changing medium three times a week was started on day 5. When the epithelial cells had grown from the primary explants, they were passaged using TrypLE Express (Gibco, Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s instructions and re-seeded into the appropriate size vessel for a 2500 cells/cm2 density.
Growth protocol The initial growth medium (KM) was according to Southgate: Keratinocyte Growth Medium with 5 ng/ml recombinant human epidermal growth factor (EGF), 50 ?g/ml bovine pituitary extract (all from Gibco) and 30 ng/ml cholera toxin (Sigma, St. Louis, MO). To induce differentiation, medium was changed two days before extraction to a high-calcium, serum-containing medium (DM) described by Keay: DMEM-F12 (Media Tech, Herndon, VA) with 10% fetal bovine serum , 1% antibiotic/antimycotic solution, 1% L-glutamine, 1.0 U/ml insulin (all from Sigma), and 5 ?g/ml hEGF (R & D Systems, Minneapolis, MN). Total RNA was extracted from cells at passages 3 to 6.
Extracted molecule total RNA
Extraction protocol Standard Affymetrix
Label Standard Affymetrix
Label protocol Standard Affymetrix
 
Hybridization protocol Standard Affimetrix
Scan protocol Affy
Description Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Jun 19, 2008
Last update date Aug 28, 2018
Contact name Deborah Erickson
E-mail(s) dreric2@email.uky.edu
Phone 859-323-3831
Organization name University of Kentucky
Department Surgery
Lab Urology
Street address 800 Rose Street, MS275
City Lexington
State/province KY
ZIP/Postal code 40536-0298
Country USA
 
Platform ID GPL570
Series (1)
GSE11839 Differentiation associated changes in gene expression profiles for interstitial cystitis and control urothelial cells
Relations
Reanalyzed by GSE49910
Reanalyzed by GSE119087

Data table header descriptions
ID_REF Probe Set
VALUE MAS5-calculated Signal intensity
DETECTION P-VALUE the probability that a probe set is absent, ranging from 0 to 1 (in this study, probe set with p < 0.05 were considered present)

Data table
ID_REF VALUE DETECTION P-VALUE
AFFX-BioB-5_at 431.6 0.000754
AFFX-BioB-M_at 575 0.000044
AFFX-BioB-3_at 281.2 0.00039
AFFX-BioC-5_at 396.4 0.000052
AFFX-BioC-3_at 512.2 0.000081
AFFX-BioDn-5_at 2863.4 0.000044
AFFX-BioDn-3_at 6657.2 0.000081
AFFX-CreX-5_at 15996.3 0.000052
AFFX-CreX-3_at 21009.4 0.000044
AFFX-DapX-5_at 5 0.559354
AFFX-DapX-M_at 3 0.891021
AFFX-DapX-3_at 11.5 0.5
AFFX-LysX-5_at 4.3 0.824672
AFFX-LysX-M_at 11.6 0.455413
AFFX-LysX-3_at 38.9 0.018281
AFFX-PheX-5_at 2.6 0.760937
AFFX-PheX-M_at 3.7 0.941556
AFFX-PheX-3_at 10.4 0.699394
AFFX-ThrX-5_at 3.3 0.953518
AFFX-ThrX-M_at 29.9 0.165861

Total number of rows: 54675

Table truncated, full table size 1327 Kbytes.




Supplementary file Size Download File type/resource
GSM299096.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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