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| Status |
Public on Aug 01, 2012 |
| Title |
Human cartilage zone arrays |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Objective. Identify novel genes and pathways specific to superficial (SZ), middle (MZ) and deep zones (DZ) of normal articular cartilage.
Methods. Articular cartilage was obtained from knees of 4 normal human donors. The cartilage zones were dissected on a microtome. RNA was analyzed on human genome arrays. Data obtained with human tissue were compared to bovine cartilage zone specific DNA arrays. Genes differentially expressed between zones were evaluated using direct annotation for structural or functional features, and by enrichment analysis for integrated pathways or functions.
Results. The greatest differences were observed between SZ and DZ in both human and bovine cartilage. The MZ was transitional between the SZ and DZ and thereby shared some of the same pathways as well as structural/functional features of the adjacent zones. Cellular functions and biological processes enriched in the SZ relative to the DZ, include most prominently ECM receptor interactions, cell adhesion molecules, regulation of actin cytoskeleton, ribosome-related functions and signaling aspects such as Interferon gamma, IL4, CDC42Rac and Jak-Stat. Two pathways were enriched in the DZ relative to the SZ, including PPARG and EGFR_SMRTE.
Conclusion. These differences in cartilage zonal gene expression identify new markers and pathways that govern the unique differentiation status of chondrocyte subpopulations.
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| Overall design |
12 samples, 4 donors, 3 conditions each donor (SZ, MZ and DZ), 0 donor replicates, comparisons made between SZ, MZ and DZ to identify differentially expressed genes.
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| Contributor(s) |
Grogan SP, Duffy SF, Pauli C, Koziol JA, Su A, D'Lima DD, Lotz MK |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Aug 01, 2012 |
| Last update date |
Jul 26, 2018 |
| Contact name |
Shawn Patrick Grogan |
| E-mail(s) |
sgrogan@scripps.edu
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| Phone |
8587848955
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| Fax |
8587842744
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| Organization name |
TSRI
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| Department |
MEM
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| Lab |
MEM-161
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| Street address |
10550 N. Torrey Pines Road, MEM161
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platforms (1) |
| GPL6244 |
[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] |
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| Samples (12)
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| GSM979412 |
normal (grade 1) cartilage, deep zone, rep 1 |
| GSM979413 |
normal (grade 1) cartilage, mid zone, rep 1 |
| GSM979414 |
normal (grade 1) cartilage, superficial zone, rep 1 |
| GSM979415 |
normal (grade 1) cartilage, deep zone, rep 2 |
| GSM979416 |
normal (grade 1) cartilage, mid zone, rep 2 |
| GSM979417 |
normal (grade 1) cartilage, superficial zone, rep 2 |
| GSM979418 |
normal (grade 1) cartilage, deep zone, rep 3 |
| GSM979419 |
normal (grade 1) cartilage, mid zone, rep 3 |
| GSM979420 |
normal (grade 1) cartilage, superficial zone, rep 3 |
| GSM979421 |
normal (grade 1) cartilage, deep zone, rep 4 |
| GSM979422 |
normal (grade 1) cartilage, mid zone, rep 4 |
| GSM979423 |
normal (grade 1) cartilage, superficial zone, rep 4 |
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| This SubSeries is part of SuperSeries: |
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| Relations |
| BioProject |
PRJNA171733 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE39795_RAW.tar |
44.6 Mb |
(http)(custom) |
TAR (of CEL) |
| GSE39795_matrix_dCHIP.txt.gz |
674.8 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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