|
| Status |
Public on Aug 01, 2015 |
| Title |
Donor 4 - 09FC45 - 50% confluence - mAdbID:107357 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
EBV-infected lymphcytes
|
| Organisms |
Homo sapiens; human gammaherpesvirus 4 |
| Characteristics |
cell type: Lymphoblastoid cells transfected with Epstein-Barr virus (EBV)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol RNA Extraction Protocol
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturer's 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 |
hy3
|
| Label protocol |
Hy3 Labeling Protocol
Other: 4 µg total RNA was directly labeled with miRCURY(TM) LNA Array Power Labeling Kit (Exiqon, Woburn, MA) according to manufacture's procedure.
|
| |
|
| Channel 2 |
| Source name |
Donor 4 - 09FC45
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone Marrow
cell type: Bone Marrow Stromal Cell (BMSC)
individual: 09FC45
|
| Treatment protocol |
In-vitro treatment: Bone marrow collection and BMSC culture were performed. Passage 2 BMSCs from 7 consenting donors were thawed from a working cell bank and plated at a density of 3 x 103/cm2 in T-75 flasks (Corning Life Sciences, Corning, NY), the cells were cultured to passage 3 with complete culture medium [alpha MEM with 2 mM glutamine (Lonza, Walkersville, MD, USA), supplemented with 20% lot-selected FBS (Hyclone, Thermo Fischer Scientific, Waltham, MA) and 10 ug/ml Gentamicin]. Upon reaching 80% confluence, passage 3 BMSCs were lifted by TryPLE Express (Invitrogen, Life Technologies, Grand Island, NY) and sub-cultured at the same density. When the cells reached 50%, 80% and 100% confluence as determined by microscope observation, they were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol RNA Extraction Protocol
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturer's 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 |
hy5
|
| Label protocol |
Hy5 Labeling Protocol
Other: 4 µg total RNA was directly labeled with miRCURY(TM) 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: 3.22;; 4.56
Temperature: 31.45
|
| Description |
mAdb experiment ID: 107357
|
| Data processing |
miRNA Data Processing
Calculation Method: The signal intensities and logRatio were exported into BRRArray Tools, and median-normalized.
|
| |
|
| Submission date |
Aug 15, 2014 |
| Last update date |
Aug 01, 2015 |
| Contact name |
Jiaqiang Ren |
| E-mail(s) |
renj@mail.nih.gov
|
| Phone |
301-435-4810
|
| Organization name |
National Institutes of Health
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19084 |
| Series (1) |
| GSE60449 |
A Global Transcriptome Analysis of BMSC from different confluences, But Gene Expression Profiling Suggested Comprised Pro-angiogenesis Effects |
|
