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| Status |
Public on Sep 05, 2008 |
| Title |
Differentiation associated changes in gene expression profiles for interstitial cystitis and control urothelial cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
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| Summary |
Purpose: Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells. Materials and Methods: Bladder biopsies were taken from IC patients and controls (women having surgery for stress incontinence). Primary cultures were grown in Keratinocyte Growth Medium with supplements. To induce differentiation, in some plates the medium was changed to DMEM-F12 with supplements. RNA was analyzed with Affymetrix chips. Three nonulcer IC patients were compared with three controls. Results: After inducing differentiation, 302 genes with a described function were altered at least 3-fold with p <0.01 in both IC and control cells. Functions of the162 upregulated genes included cell adhesion (e.g. claudins, occludin, cingulin); urothelial differentiation, retinoic acid pathway and keratinocyte differentiation (e.g. skin cornified envelope components). The 140 downregulated genes included genes associated with basal urothelium (e.g. p63, integrins ?4, ?5 and ?6, basonuclin 1 and extracellular matrix components), vimentin, metallothioneins and members of the Wnt and Notch pathways. Comparing IC vs. control cells after differentiation, only seven genes with a described function were altered at least 3-fold with p <0.01. PI3, SERPINB4, CYP2C8, EFEMP2 and SEPP1 were decreased in IC; AKR1C2 and MKNK1 were increased in IC. Conclusions: Differentiation-associated changes occurred in both IC and control cells. Comparing IC vs. control revealed very few differences. This study may have included IC patients with minimal urothelial deficiency and/or selected the cells that were most robust in culture. Also, the abnormal urothelium in IC may be due to post-translational changes and/or the bladder environment.
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| Overall design |
Human female urothelial cell cultures, differentiated vs. non-differentiated,interstitial cystitis vs. control
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| Contributor(s) |
Erickson DR, Schwarze S, Dixon JK, Clark CJ, Hersh MA |
| Citation(s) |
18951569 |
| Submission date |
Jun 19, 2008 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Deborah Erickson |
| E-mail(s) |
dreric2@email.uky.edu
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| Phone |
859-323-3831
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| Organization name |
University of Kentucky
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| Department |
Surgery
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| Lab |
Urology
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| Street address |
800 Rose Street, MS275
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| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40536-0298 |
| Country |
USA |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (12)
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| GSM299095 |
human cultured bladder HB DM, subject 8 |
| GSM299096 |
human cultured bladder HB DM, subject 12 |
| GSM299097 |
human cultured bladder HB DM, subject 13 |
| GSM299098 |
human cultured bladder HB KM, subject 8 |
| GSM299099 |
human cultured bladder HB KM, subject 12 |
| GSM299100 |
human cultured bladder HB KM, subject 13 |
| GSM299101 |
human cultured bladder IC DM, subject 1 |
| GSM299102 |
human cultured bladder IC DM, subject 3 |
| GSM299103 |
human cultured bladder IC DM, subject 10 |
| GSM299104 |
human cultured bladder IC KM, subject 1 |
| GSM299105 |
human cultured bladder IC KM, subject 3 |
| GSM299106 |
human cultured bladder IC KM, subject 10 |
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| Relations |
| BioProject |
PRJNA105631 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE11839.pdf |
15.0 Kb |
(ftp)(http) |
PDF |
| GSE11839_RAW.tar |
60.8 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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