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Sample GSM307484 Query DataSets for GSM307484
Status Public on Apr 17, 2009
Title TE06 (I6) - replicate 4 - mAdbID:94643
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: 33;; 10
LaserPower: 3.22;; 4.12
Temperature: 29.78
Description mAdb experiment ID: 94643
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 -0.490572333 1 1 1 2048 1388 118 167 2554 1781 109 139 0
6519981_1 -1.121527672 1 1 2 317 254 79 147 446 314 94 141 0
6520077_1 1.541930199 1 1 3 491 321 139 190 184 215 94 153 0
6520173_1 -0.535041928 1 1 4 177 163 112 150 149 136 104 158 -50
6520269_1 NULL 1 1 5 188 172 124 145 151 135 92 154 -50
6520365_1 NULL 1 1 6 168 177 114 170 143 130 101 148 -50
6520461_1 NULL 1 1 7 189 137 112 159 151 134 97 154 -50
6520557_1 NULL 1 1 8 2314 2074 125 188 1092 1040 85 142 0
6519885_2 -0.490572333 1 2 1 1881 1423 128 169 2340 1534 105 154 0
6519981_2 -1.121527672 1 2 2 166 149 117 159 289 301 100 149 -50
6520077_2 1.541930199 1 2 3 245 280 115 157 145 137 96 152 -50
6520173_2 -0.535041928 1 2 4 199 261 110 173 180 182 101 153 -50
6520269_2 NULL 1 2 5 184 198 116 173 147 162 88 149 -50
6520365_2 NULL 1 2 6 164 142 120 156 154 141 105 143 -50
6520461_2 NULL 1 2 7 180 162 117 145 121 112 121 155 -50
6520557_2 NULL 1 2 8 1560 1750 122 141 1079 1105 102 146 0
6519889_1 0.247355685 1 3 1 897 639 123 167 508 345 104 144 0
6519985_1 0.727193952 1 3 2 874 939 118 168 388 273 97 168 0
6520081_1 -0.333726048 1 3 3 157 131 112 150 150 145 99 162 -50
6520177_1 0.335502952 1 3 4 168 162 117 162 116 119 112 153 -50

Total number of rows: 1712

Table truncated, full table size 102 Kbytes.




Supplementary file Size Download File type/resource
GSM307484.gpr.gz 176.6 Kb (ftp)(http) GPR
Processed data included within Sample table
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