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GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 23, 2008 |
| Title |
5-Aza hMSCs replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
bone marrow derived
|
| Organism |
Homo sapiens |
| Characteristics |
hMSCs exposed to 5-Azacytidine
|
| Biomaterial provider |
own
|
| Treatment protocol |
Cells were exposed to 5-Azacytidine and cultured for 21 days. Media was changed every 3 days.
|
| Growth protocol |
standard cell culture condition (95% air, 5% CO2, 37C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy kit from Qiagen
|
| Label |
Biotin
|
| Label protocol |
Synthesis of Biotin-Labeled cRNA/Purification
ENZO BioArray RNA Transcript Labeling Kit
GeneChip Sample Cleanup Module
Miscellaneous Reagents/Supplies
100% ethanol at room temperature
80% ethanol at room temperature
Water, Molecular Biology Grade or DEPC-treated
Ethidium Bromide
Sterile, RNase-free, microcentrifuge tubes, 1.5mL
Micropipettors
Sterile-barrier, RNase-free pipette tips
Mini agarose gel electrophoresis unit with appropriate buffers
UV Spectrophotometer
Cooling water bath
|
| |
|
| Hybridization protocol |
Water, Molecular Biology Grade or DEPC-treated
Acetylated Bovine Serum Albumin (BSA) solution (50 mg/mL)
Herring Sperm DNA
GeneChip Eukaryotic Hybridization Control Kit
5M NaCl, RNase-free, DNase-free
MES Free Acid Monohydrate
MES Sodium Salt
EDTA Disodium Salt
Miscellaneous Reagents/Supplies
Surfact-Amps 20 (Tween-20), 10%
Hybridization Oven 640
Sterile, RNase-free, microcentrifuge tubes, 1.5mL
Micropipettors
Sterile-barrier pipette tips and non-barrier tips
Heatblock
|
| Scan protocol |
Washing, Staining, and Scanning
Water, Molecular Biology Grade
Distilled water
Acetylated Bovine Serum Albumin (BSA) solution (50 mg/mL)
R-Phycoerythrin Streptavidin
20X SSPE (3M NaCl, 0.2M NaH2PO4, 0.02M EDTA)
Goat IgG, Reagent Grade
Anti-streptavidin antibody (goat), biotinylated
10% surfact-Amps 20 (Tween-20)
|
| Description |
Samples were processed in CINJ Core Expression Array Facility according to Affymetrix protocol
|
| Data processing |
MAS5.0
|
| |
|
| Submission date |
Dec 03, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Pravin Mishra |
| E-mail(s) |
[email protected]
|
| Organization name |
UMDNJ
|
| Department |
Pharmacology
|
| Lab |
Bertino/Banerjee
|
| Street address |
195 Little Albany St.
|
| City |
New Brunswick |
| State/province |
NJ |
| ZIP/Postal code |
08904 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE9764 |
Carcinoma Associated Fibroblast Like Differentiation of Human Mesenchymal Stem Cells |
|
| Relations |
| Reanalyzed by |
GSE119087 |
| Data table header descriptions |
| ID_REF |
|
| VALUE |
fluorescence intensity |
| ABS_CALL |
quality: present, absent, marginal |
| DETECTION P-VALUE |
statistical significance |
| Data table |
| ID_REF |
VALUE |
ABS_CALL |
DETECTION P-VALUE |
| AFFX-BioB-5_at |
193.347 |
P |
0.000509415 |
| AFFX-BioB-M_at |
285.297 |
P |
6.02111e-05 |
| AFFX-BioB-3_at |
191.25 |
P |
0.000169227 |
| AFFX-BioC-5_at |
599.252 |
P |
5.16732e-05 |
| AFFX-BioC-3_at |
716.577 |
P |
4.42873e-05 |
| AFFX-BioDn-5_at |
1370.17 |
P |
4.42873e-05 |
| AFFX-BioDn-3_at |
2842.35 |
P |
0.00010954 |
| AFFX-CreX-5_at |
7365.47 |
P |
5.16732e-05 |
| AFFX-CreX-3_at |
7725.32 |
P |
4.42873e-05 |
| AFFX-DapX-5_at |
6.00412 |
A |
0.368438 |
| AFFX-DapX-M_at |
3.10184 |
A |
0.724854 |
| AFFX-DapX-3_at |
1.15264 |
A |
0.973899 |
| AFFX-LysX-5_at |
3.52545 |
A |
0.5 |
| AFFX-LysX-M_at |
2.1528 |
A |
0.686277 |
| AFFX-LysX-3_at |
6.55489 |
A |
0.123572 |
| AFFX-PheX-5_at |
2.17466 |
A |
0.916408 |
| AFFX-PheX-M_at |
0.419603 |
A |
0.98333 |
| AFFX-PheX-3_at |
22.7492 |
A |
0.227636 |
| AFFX-ThrX-5_at |
10.2025 |
A |
0.382599 |
| AFFX-ThrX-M_at |
1.34894 |
A |
0.852061 |
Total number of rows: 54675
Table truncated, full table size 1629 Kbytes.
| Supplementary file |
Size |
Download |
File type/resource |
| GSM246359.CEL.gz |
5.2 Mb |
(ftp)(http) |
CEL |
| GSM246359.CHP.gz |
296.8 Kb |
(ftp)(http) |
CHP |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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