|
| Status |
Public on Apr 17, 2009 |
| Title |
WA09 (H9) - replicate 3 - mAdbID:94794 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Pooled Normal Donor PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: blood
Cell type: PBMC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Extraction Protocol
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.
|
| Label |
cy3
|
| Label protocol |
Cy3 Labeling Protocol
Other: Labeled using ULS aRNA Fluorescent Labeling kit (Kreatech).
|
| |
|
| Channel 2 |
| Source name |
WA09 (H9)
|
| Organism |
Homo sapiens |
| Characteristics |
Cell line: WA09 (H9)
Cell type: Human embryonic stem cell line
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Extraction Protocol
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.
|
| Label |
cy5
|
| Label protocol |
Cy5 Labeling Protocol
Other: Labeled using ULS aRNA Fluorescent Labeling kit (Kreatech).
|
| |
|
| |
| Hybridization protocol |
Hybridization Protocol
Other: Hybridization: Combine Cy3 and Cy5 labeled target (adjust the color to purple) and complete dry the sample by speed vacuum . Add 37ul of the following mixture to the dried target (for 20x40mm slide): 1ul 50x Denhardt’s blocking solution (Sigma Cat# 2532) 1ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 1ul yeast tRNA (4mg/ml Sigma Cat# R8759) 10ul Human Cot I DNA (1mg/ml Gibco BRL Cat# 15279-011) 3ul 20X SSC 1ul 10% SDS 20ul of DEPC H2O Heat for 2 min at 99oC and Cool to RT. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 65oC over night.
|
| Scan protocol |
Creator: GenePix Pro 4.0.1.17
Scanner: GenePix 4000B [84945]
ScanPower: 33;; 10
LaserPower: 3.18;; 4.21
Temperature: 28.07
|
| Description |
mAdb experiment ID: 94794
|
| Data processing |
BRB ArrayTool Data Processing
Calculation Method: Analyzed using BRBArrayTools developed by the Biometric Research Branch, National Cancer Institute (http://linus.nci.nih.gov/BRB-ArrayTools.html ). Briefly, the raw data set was filtered according to standard procedure to exclude spots with minimum intensity that arbitrarily was set to an intensity parameter of 200 for in both fluorescence channels. If the fluorescence intensity of one channel was great than 200 and that of the other but was below 200, the fluorescence of the low intensity channel was arbitrarily set to 200. Spots with diameters < 20ìm and flagged spots were also excluded from the analyses. Then, the filtered data were normalized using Lowess Smoother for gene expression microarray.
|
| |
|
| Submission date |
Jul 24, 2008 |
| Last update date |
Apr 17, 2009 |
| Contact name |
Francesco Maria Marincola |
| E-mail(s) |
[email protected]
|
| Phone |
301-793-8210
|
| Organization name |
Sidra Medical and Research Center
|
| Street address |
Al Nasr Tower, AL Corniche Street, PO Box 26999
|
| City |
Doha |
| ZIP/Postal code |
PO Box 26999 |
| Country |
Qatar |
| |
|
| Platform ID |
GPL7088 |
| Series (3) |
| GSE12228 |
Gene expression profiling among human embryonic stem cells, differerentiated EBs and adult cells |
| GSE12250 |
Human embryonic stem cells, differerentiated EBs and adult cells |
| GSE20431 |
Gene expression profiling on FePro labeled bone marrow stromal cells |
|
| Data table header descriptions |
| ID_REF |
NCI mAdb well id plus replicate number |
| VALUE |
log2 of the Calibrated Ratio (Cy5 channel/Cy3 channel) |
| Slide_block |
Array block location |
| Slide_column |
Array column location |
| Slide_row |
Array row location |
| CY5_mean |
Red Channel Sample mean Signal (Background Subtracted) |
| CY5_SD |
Red Channel Sample Standard Deviation |
| CY5_BKD_median |
Red Channel Sample median Background Level |
| CY5_BKD_SD |
Red Channel Sample Background Standard Deviation |
| CY3_mean |
Green Channel Sample mean Signal (Background Subtracted) |
| CY3_SD |
Green Channel Sample Standard Deviation |
| CY3_BKD_median |
Green Channel Sample median Background Level |
| CY3_BKD_SD |
Green Channel Sample Background Standard Deviation |
| Flag |
Quality flag 0->good, -50->Not found, -100->Bad |
