|
| Status |
Public on Apr 17, 2009 |
| Title |
H9-EB-day4 - mAdbID:93533 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
EBV-infected lymphcytes
|
| Organism |
Homo sapiens |
| Characteristics |
Cell type: Lymphoblastoid cells transfected with Epstein-Barr virus (EBV)
|
| 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: 4 µg total RNA was directly labeled with miRCURY™ LNA Array Power Labeling Kit (Exiqon, Woburn, MA) according to manufacture’s procedure.
|
| |
|
| Channel 2 |
| Source name |
WA09 (H9) - differentiation day 4
|
| Organism |
Homo sapiens |
| Characteristics |
Cell line: WA09 (H9)
Cell type: Human embryonic stem cell line
|
| Treatment protocol |
Treatment time: day 4
In-vivo treatment: For embryonic body (EB) differentiation, hES cells were detached with collagenase IV and the cell aggregates were briefly triturated and cultured in ultra low attachment plates (Corning Inc, Corning, NY) for 4 days in maintenance medium without bFGF. The medium was changed every three days.
|
| 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: 4 µg total RNA was directly labeled with miRCURY™ LNA Array Power Labeling Kit (Exiqon, Woburn, MA) according to manufacture’s procedure.
|
| |
|
| |
| Hybridization protocol |
Sample Hybridization Protocol
Other: The samples and the reference were co-hybridized to the miRNA array at room temperature over night. Both the processed cDNA and the miRNA array slides were scanned by GenePix scanner Pro 4.0 (Axon, Sunnyvale, CA, USA).
|
| Scan protocol |
Creator: GenePix Pro 4.0.1.17
Scanner: GenePix 4000B [84945]
ScanPower: 10;; 10
LaserPower: 3.24;; 4.1
Temperature: 29.68
|
| Description |
mAdb experiment ID: 93533
|
| Data processing |
miRNA Data Processing
Calculation Method: The signal intensities were exported by R-based package mArray; the background-substracted intensities were normalized by variance stabilization normalization (VSN)and imported into BRRArray Tools.
|
| |
|
| Submission date |
Jul 24, 2008 |
| Last update date |
Apr 17, 2009 |
| Contact name |
Francesco Maria Marincola |
| E-mail(s) |
fmarincola@sidra.org
|
| 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 |
GPL7089 |
| Series (2) |
| GSE12229 |
microRNA expression profiling among human embryonic stem cells, differerentiated EBs and adult cells |
| GSE12250 |
Human embryonic stem cells, differerentiated EBs and adult 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 |
