|
| Status |
Public on Aug 10, 2005 |
| Title |
hMSCsVsLiver2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Untreated Mesenchymal Stem Cells
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: isolated hMSC
Gender: male
Age: comprised between 35 and 50
Donor #2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini kit (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
Representational amplification of mRNA and fluorescent labelling was carried out using Ambion’s Amino Allyl MessageAmp aRNA kit and NHS ester Cy3 and Cy5 conjugated fluorescent dyes (Amersham Bioscience) following the protocol suggested by the supplier
|
| |
|
| Channel 2 |
| Source name |
Adult liver
|
| Organism |
Homo sapiens |
| Characteristics |
Human liver
Chemicon cat.Nr 562
|
| Biomaterial provider |
Chemicon
|
| Extracted molecule |
total RNA |
| Label |
Cy5
|
| Label protocol |
Representational amplification of mRNA and fluorescent labelling was carried out using Ambion’s Amino Allyl MessageAmp aRNA kit and NHS ester Cy3 and Cy5 conjugated fluorescent dyes (Amersham Bioscience) following the protocol suggested by the supplier
|
| |
|
| |
| Hybridization protocol |
The arrays were pre-blocked in hybridization buffer (5X SSC; 0.1%SDS; 0.2 mg/ml Torula Yeast RNA; 5X Denhardt's solution; 25% formamide) for 2 hours. 120 pmol of each dye-labeled aRNA sample, diluted in 100 µl of hybridization buffer were pre-denatured for 5 minutes at 65°C and then applied on the glass slide. A glass coverslip was used to uniformly spread the sample solution. Incubation was carried on for 24 hours at 48°C in a humid chamber and was followed by 6 washing steps with lowering concentration of SSC and SDS
|
| Scan protocol |
Array scanning was performed by using a ScanArray Lite (PerkinElmer Life Sciences) Laser Power= 75; PMT(Cy3)=85; PMT(Cy5)=80, resolution 5 µm/pixel.
|
| Description |
TIFF images were analysed with TIGR Spotfinder v2.2.4. (from TIGR TM4 suite; Saeed et al., Biotechniques 34(2): 374-8. 2003) using Otsu thresholding with min SpotSize=10; maxSpotSize=55
|
| Data processing |
Non linear LOWESS based lockfit alogorithm employing MIDAS (from TIGR TM4 suite; Saeed et al., 2003)
|
| |
|
| Submission date |
Jun 07, 2005 |
| Last update date |
Oct 28, 2005 |
| Contact name |
Paolo Malatesta |
| E-mail(s) |
[email protected]
|
| Phone |
+390105558403
|
| Organization name |
IRCCS Ospedale Policlinico San Martino
|
| Street address |
Largo Rosanna Benzi 10
|
| City |
Genoa |
| ZIP/Postal code |
16132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL2136 |
| Series (1) |
| GSE2776 |
Neurogenic potential of human mesenchymal stem cells revisited |
|
