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Sample GSM60451 Query DataSets for GSM60451
Status Public on Aug 10, 2005
Title hMSCsVsLiver3
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 #3
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) paolo.malatesta@unige.it
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

Data table header descriptions
ID_REF
VALUE log2(NormCH2/NormCH1) where NormCH1 and NormCH2 are respectively the value of CH1_SIG_MEAN and CH2_SIG_MEAN after lockfit normalization with MIDAS
CH1_SIG_MEAN Spot intensity in channel 1 corrected for background as output of TIGR spotfinder
CH1_BKD_MEAN
CH2_SIG_MEAN Spot intensity in channel 2 corrected for background as output of TIGR spotfinder
CH1_BKD_MEAN Spot background in channel 1 as output from TIGR Spotfinder

Data table
ID_REF VALUE CH1_SIG_MEAN CH1_BKD_MEAN CH2_SIG_MEAN CH1_BKD_MEAN
1 0.010703398 1745893 154056 1157147 216188
2 0.261351016 1732472 155976 1360160 231954
3 0.12511878 1918430 155976 1367618 224316
4 0.230415451 1868793 152712 1432642 226442
5 0.107739789 1981731 129843 1394721 200151
6 0.08047288 1707291 115878 1187483 180048
7 0.096162457 1698407 110670 1194203 163710
8 0.117701818 1814303 107868 1289617 177466
9 0.182596986 1772377 114625 1317831 184625
10 0.247983089 1677740 114896 1307380 187040
11 0.26090462 2575077 124081 2004473 179191
12 0.150399043 1847330 112404 1341569 167388
13 -0.077734856 1854323 109550 1153781 181650
14 0.045631419 1951653 112057 1317172 169338
15 0.035113783 1938701 94875 1299396 163680
16 -0.143609002 1673055 101231 1004777 163254
17 0.287526025 2693014 120835 2133932 184886
18 0.189311968 1889298 121278 1407823 179916
19 0.091419104 1793323 107087 1252925 183034
20 0.120687817 1808039 114180 1287968 175890

Total number of rows: 46752

Table truncated, full table size 1825 Kbytes.




Supplementary data files not provided

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