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Sample GSM1480282 Query DataSets for GSM1480282
Status Public on Aug 01, 2015
Title Donor 3 - 09FC44 - 50% confluence - mAdbID:107354
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 3 - 09FC44
Organism Homo sapiens
Characteristics tissue: Bone Marrow
cell type: Bone Marrow Stromal Cell (BMSC)
individual: 09FC44
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: 3.21;; 4.53
Temperature: 31.09
Description mAdb experiment ID: 107354
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

Data table header descriptions
ID_REF mAdb well id plus replicate number
VALUE log ratio (log2 of CY5 channel/CY3 channel)

Data table
ID_REF VALUE
7257482_1 -2.671
7257483_1
7257484_1
7257485_1 -3.218
7257486_1
7257487_1 1.036
7257488_1 1.093
7257489_1 -0.388
7257490_1 2.092
7257491_1
7257492_1 1.500
7257493_1 1.406
7257494_1 1.380
7257495_1
7257496_1 1.592
7257497_1
7257498_1 0.659
7257499_1 -0.551
7257500_1 0.979
7257501_1

Total number of rows: 1920

Table truncated, full table size 22 Kbytes.




Supplementary file Size Download File type/resource
GSM1480282_107354.gpr.gz 317.5 Kb (ftp)(http) GPR
Processed data included within Sample table

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