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Sample GSM307487 Query DataSets for GSM307487
Status Public on Apr 17, 2009
Title H9-EB-day7 - replicate 2 - mAdbID:94649
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 WA09 (H9) - differentiation day 7
Organism Homo sapiens
Characteristics Cell line: WA09 (H9)
Cell type: Human embryonic stem cell line
Treatment protocol Treatment time: day 7
In-vivo treatment: For embryonic body (EB) differentiation, hES cells were detached with collagenase IV and the cell aggregates were briefly triturated and cultured in ultra low attachment plates (Corning Inc, Corning, NY) for 7 days in maintenance medium without bFGF. The medium was changed every three days.
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;; 4.76
Temperature: 27.21
Description mAdb experiment ID: 94649
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 0.458197832 1 1 1 3015 1823 38 125 2997 1662 43 48 0
6519981_1 0.544932663 1 1 2 263 282 37 162 209 195 38 48 0
6520077_1 0.409417987 1 1 3 179 185 36 115 74 58 39 45 0
6520173_1 -0.062123984 1 1 4 100 124 38 154 64 48 41 50 -50
6520269_1 NULL 1 1 5 108 128 37 124 68 59 41 44 -50
6520365_1 NULL 1 1 6 98 138 37 129 71 52 39 47 -50
6520461_1 NULL 1 1 7 102 119 37 121 61 44 42 43 -50
6520557_1 NULL 1 1 8 403 461 37 117 292 307 39 44 0
6519885_2 0.458197832 1 2 1 3140 1797 39 245 3026 1400 42 107 0
6519981_2 0.544932663 1 2 2 204 222 38 136 204 167 48 50 0
6520077_2 0.409417987 1 2 3 166 215 38 146 88 67 39 50 0
6520173_2 -0.062123984 1 2 4 98 113 38 118 59 40 41 48 -50
6520269_2 NULL 1 2 5 117 146 38 112 70 60 48 48 -50
6520365_2 NULL 1 2 6 172 171 37 143 90 87 46 41 0
6520461_2 NULL 1 2 7 102 149 38 135 68 54 41 60 -50
6520557_2 NULL 1 2 8 193 297 37 120 120 203 41 47 0
6519889_1 0.6139431 1 3 1 461 387 38 133 331 180 47 46 0
6519985_1 0.49865824 1 3 2 160 174 40 147 142 100 43 53 0
6520081_1 -0.269443601 1 3 3 105 153 38 128 67 50 44 48 -50
6520177_1 0.733891726 1 3 4 117 136 39 128 75 65 50 52 -50

Total number of rows: 1712

Table truncated, full table size 94 Kbytes.




Supplementary file Size Download File type/resource
GSM307487.gpr.gz 165.9 Kb (ftp)(http) GPR
Processed data included within Sample table
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