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Sample GSM307489 Query DataSets for GSM307489
Status Public on Apr 17, 2009
Title LFB - mAdbID:94651
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 LFB
Organism Homo sapiens
Characteristics Tissue: lung
Cell type: Lung fibroblast
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: 3.2;; 5.1
Temperature: 26.69
Description mAdb experiment ID: 94651
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

Data table
ID_REF VALUE Slide_block Slide_column Slide_row CY5_mean CY5_SD CY5_BKD_median CY5_BKD_SD CY3_mean CY3_SD CY3_BKD_median CY3_BKD_SD Flag
6519885_1 -2.296218395 1 1 1 323 304 34 114 5919 3583 46 71 0
6519981_1 1.499215364 1 1 2 209 274 35 114 229 313 42 79 0
6520077_1 -0.845425129 1 1 3 69 80 34 128 74 59 37 63 -50
6520173_1 -0.26642698 1 1 4 100 119 34 117 90 75 41 65 -50
6520269_1 NULL 1 1 5 71 94 34 275 82 80 41 295 -50
6520365_1 NULL 1 1 6 89 119 34 114 80 77 38 78 -50
6520461_1 NULL 1 1 7 97 127 33 114 81 75 47 65 -50
6520557_1 NULL 1 1 8 125 155 35 140 599 509 36 133 0
6519885_2 -2.296218395 1 2 1 334 295 35 106 5844 3425 39 77 0
6519981_2 1.499215364 1 2 2 202 203 33 93 312 499 34 64 0
6520077_2 -0.845425129 1 2 3 61 70 34 124 89 78 34 58 -50
6520173_2 -0.26642698 1 2 4 102 135 34 117 89 73 45 70 -50
6520269_2 NULL 1 2 5 73 105 34 115 89 74 38 62 -50
6520365_2 NULL 1 2 6 91 108 35 144 91 77 42 66 -50
6520461_2 NULL 1 2 7 99 124 34 121 76 70 42 68 -50
6520557_2 NULL 1 2 8 195 223 33 99 403 620 43 69 0
6519889_1 -0.224527985 1 3 1 284 348 34 120 464 288 40 556 0
6519985_1 -0.483018696 1 3 2 129 170 34 113 119 98 41 66 -50
6520081_1 -0.100152299 1 3 3 80 109 35 129 83 77 38 76 -50
6520177_1 -0.078846753 1 3 4 77 124 35 108 88 87 46 62 -50

Total number of rows: 1712

Table truncated, full table size 95 Kbytes.




Supplementary file Size Download File type/resource
GSM307489.gpr.gz 165.2 Kb (ftp)(http) GPR
Processed data included within Sample table
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