|
| Status |
Public on Apr 05, 2007 |
| Title |
Umbilical cord blood cells transcriptome - T00234774 |
| Sample type |
RNA |
| |
|
| Source name |
Umbilical cord blood cells
|
| Organism |
Homo sapiens |
| Characteristics |
Freshly isolated CD133+/CD34+ umbilical cord blood cells prior to cultivation.
|
| Extracted molecule |
total RNA |
| Label |
Cy5
|
| |
|
| Description |
Human Umbilical Cord Blood cells was collected from full-term deliveries with written informed consent approved by the Internal Review Board of the Albert Einstein Hospital (n=5). Mononuclear cells were isolated by density gradient using Ficoll-PaqueTM PLUS (Amersham Pharmacia Biotech). CD133+ and CD34+ cells were purified by immunomagnetic separation with MiniMACS kit (Miltenyi Biotech), following the manufacturer’s protocol. The purity of isolated CD133+/CD34+ cells was generally greater than 90%, as evaluated by flow cytometry using a FACS Aria (Becton Dickinson). Total RNA was treated with RNAse free-DNAse and further purified with RNeasy spin columns (Qiagen). Hybridizations were carried out with oligonucleotide CodeLink™ Bioarrays (GE Healthcare) following the manufacturer’s protocol. One microgram of total RNA was reverse transcribed in the presence of T7- oligo dT primer. The resulting cDNA was used for in vitro transcription reaction using T7 RNA polymerase and biotinylated dUTP. Ten micrograms of target cDNA was fragmented at 94 °C for 20 min and hybridized to the bioarrays at 37°C for 18 h, under 300 rpm agitation. After staining with streptavidin-conjugated Cyanine-5 dye, the slides were washed and the fluorescence was measured. The fluorescence was measured using an Axon GenePix 4000B Scanner (Axon Instruments Inc).
|
| Data processing |
All the data processing was done by CodeLink™ Bioarrays software using default parameters set by the manufacturer.
|
| |
|
| Submission date |
Mar 16, 2006 |
| Last update date |
Apr 05, 2006 |
| Contact name |
Ricardo Z.N. Vêncio |
| Organization name |
Universidade de São Paulo
|
| Department |
Computing and Mathematics Department
|
| Lab |
http://labpib.fmrp.usp.br
|
| Street address |
Av. Bandeirantes, 3900
|
| City |
Ribeirao Preto |
| State/province |
SP |
| ZIP/Postal code |
14049-900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL2895 |
| Series (1) |
| GSE4609 |
Transcriptome analysis of Stem Cells from Human Umbilical Cord Blood |
|
| Data table header descriptions |
| ID_REF |
|
| Raw_intensity |
The background subtracted fluorescence intensity. |
| VALUE |
The normalized fluorescence intensity. |
| Quality_flag |
L = low intensity; G = good; X = mask by the manufacturer; C = contaminated |
| Signal_strength |
The fluorescence signal strength. |
| Logical_row |
Slide's row in wich the spot is placed. |
| Logical_col |
Slide's column in wich the spot is placed. |
| Center_X |
X Position of the spot, in pixels |
| Center_Y |
Y Position of the spot, in pixels |
| Spot_mean |
Foreground mean fluorescence intensity. |
| Spot_median |
Foreground median fluorescence intensity. |
| Spot_stdev |
Standard deviation of the fluorescence intensity. |
| Spot_area |
Foreground total number of pixels used. |
| Spot_diameter |
Spot's diameter in pixels. |
| Spot_noise_level |
The signal-to-noise level. |
| Bkgd_mean |
Background mean fluorescence intensity. |
| Bkgd_median |
Background median fluorescence intensity. |
| Bkgd_stdev |
Background standard deviation of the fluorescence intensity. |
| Bkgd_area |
Background total number of pixels used. |
