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Sample GSM307490 Query DataSets for GSM307490
Status Public on Apr 17, 2009
Title TE06 (I6) - replicate 3 - mAdbID:94652
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 TE06 (I6)
Organism Homo sapiens
Characteristics Cell line: TE06 (I6)
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: 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: 3.18;; 5.16
Temperature: 25.84
Description mAdb experiment ID: 94652
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 -0.169349313 1 1 1 2657 1466 36 84 4710 2230 42 69 0
6519981_1 -1.445139766 1 1 2 112 116 34 80 313 316 41 50 0
6520077_1 0.122753412 1 1 3 84 98 34 95 77 67 46 51 -50
6520173_1 0.055022769 1 1 4 82 92 34 89 64 46 43 55 -50
6520269_1 NULL 1 1 5 123 114 35 84 101 67 47 58 0
6520365_1 NULL 1 1 6 78 80 34 81 61 48 44 58 -50
6520461_1 NULL 1 1 7 82 95 35 89 71 48 43 56 -50
6520557_1 NULL 1 1 8 648 757 35 76 462 636 39 68 0
6519885_2 -0.169349313 1 2 1 2686 1612 36 90 4418 2242 50 57 0
6519981_2 -1.445139766 1 2 2 103 103 38 97 239 221 48 58 0
6520077_2 0.122753412 1 2 3 87 109 35 85 62 53 43 54 -50
6520173_2 0.055022769 1 2 4 73 102 35 88 70 56 50 95 -50
6520269_2 NULL 1 2 5 77 75 34 84 60 49 40 52 -50
6520365_2 NULL 1 2 6 79 91 34 105 64 51 48 61 -50
6520461_2 NULL 1 2 7 75 87 34 74 73 60 47 52 -50
6520557_2 NULL 1 2 8 370 488 35 89 429 487 50 57 0
6519889_1 0.24805522 1 3 1 375 323 36 77 371 223 43 55 0
6519985_1 0.262584805 1 3 2 197 169 36 91 159 100 51 67 0
6520081_1 -0.777101755 1 3 3 67 74 36 82 87 82 46 55 -50
6520177_1 0.406337351 1 3 4 109 112 36 90 61 46 49 55 -50

Total number of rows: 1712

Table truncated, full table size 93 Kbytes.




Supplementary file Size Download File type/resource
GSM307490.gpr.gz 164.6 Kb (ftp)(http) GPR
Processed data included within Sample table
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