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Sample GSM307488 Query DataSets for GSM307488
Status Public on Apr 17, 2009
Title H9-EB-day14 - mAdbID:94650
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 14
Organism Homo sapiens
Characteristics Cell line: WA09 (H9)
Cell type: Human embryonic stem cell line
Treatment protocol Treatment time: day 14
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 14 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: 33;; 10
LaserPower: 3.2;; 4.25
Temperature: 29.04
Description mAdb experiment ID: 94650
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 -0.139812112 1 1 1 7512 3867 101 174 3474 1502 49 57 0
6519981_1 -0.196505651 1 1 2 317 245 98 142 188 144 43 46 0
6520077_1 0.698531806 1 1 3 169 158 99 138 72 68 43 51 -50
6520173_1 -0.809667826 1 1 4 137 139 124 152 70 54 44 44 -50
6520269_1 NULL 1 1 5 148 156 96 150 71 58 51 52 -50
6520365_1 NULL 1 1 6 145 154 73 161 74 59 51 49 -50
6520461_1 NULL 1 1 7 158 153 90 163 63 49 48 47 -50
6520557_1 NULL 1 1 8 364 330 117 218 344 407 54 51 0
6519885_2 -0.139812112 1 2 1 6157 4098 114 190 2905 1560 52 71 0
6519981_2 -0.196505651 1 2 2 426 362 128 186 241 201 49 71 0
6520077_2 0.698531806 1 2 3 160 182 97 163 61 48 45 53 -50
6520173_2 -0.809667826 1 2 4 165 153 114 435 64 45 44 144 -50
6520269_2 NULL 1 2 5 131 149 93 151 69 55 51 52 -50
6520365_2 NULL 1 2 6 181 170 107 170 69 56 49 57 -50
6520461_2 NULL 1 2 7 144 149 105 139 65 41 45 50 -50
6520557_2 NULL 1 2 8 762 690 159 224 337 306 60 120 0
6519889_1 0.091917798 1 3 1 529 328 108 162 272 174 48 52 0
6519985_1 0.155507267 1 3 2 317 237 114 144 118 91 54 54 0
6520081_1 0.588168502 1 3 3 163 156 98 197 65 50 50 53 -50
6520177_1 1.827806711 1 3 4 197 207 107 144 73 66 50 50 -50

Total number of rows: 1712

Table truncated, full table size 96 Kbytes.




Supplementary file Size Download File type/resource
GSM307488.gpr.gz 167.5 Kb (ftp)(http) GPR
Processed data included within Sample table
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