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Sample GSM307486 Query DataSets for GSM307486
Status Public on Apr 17, 2009
Title H9-EB-day10 - replicate 2 - mAdbID:94648
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 10
Organism Homo sapiens
Characteristics Cell line: WA09 (H9)
Cell type: Human embryonic stem cell line
Treatment protocol Treatment time: day 10
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 10 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: 3.21;; 4.62
Temperature: 27.61
Description mAdb experiment ID: 94648
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 0.441622555 1 1 1 1332 992 37 133 2065 1023 49 50 0
6519981_1 -1.67931664 1 1 2 110 139 36 101 172 141 40 49 0
6520077_1 0.290632218 1 1 3 79 89 36 124 62 43 43 48 -50
6520173_1 -0.443295121 1 1 4 71 96 39 146 68 53 43 50 -50
6520269_1 NULL 1 1 5 87 138 37 123 72 60 41 46 -50
6520365_1 NULL 1 1 6 89 110 36 110 64 48 41 42 -50
6520461_1 NULL 1 1 7 110 134 37 121 74 52 50 48 0
6520557_1 NULL 1 1 8 274 333 37 108 381 400 40 45 0
6519885_2 0.441622555 1 2 1 1281 780 38 130 1698 865 40 45 0
6519981_2 -1.67931664 1 2 2 110 157 38 123 108 106 43 45 -50
6520077_2 0.290632218 1 2 3 91 126 36 132 61 49 38 45 -50
6520173_2 -0.443295121 1 2 4 85 105 37 137 63 46 42 44 -50
6520269_2 NULL 1 2 5 93 139 38 126 69 63 43 49 -50
6520365_2 NULL 1 2 6 80 113 36 115 64 48 42 47 -50
6520461_2 NULL 1 2 7 156 169 36 104 82 57 47 41 0
6520557_2 NULL 1 2 8 191 229 37 149 215 324 41 45 0
6519889_1 0.517460167 1 3 1 241 239 38 138 235 150 41 50 0
6519985_1 -0.186323106 1 3 2 160 154 39 155 124 119 48 66 0
6520081_1 0.36674419 1 3 3 93 109 37 126 63 45 39 48 -50
6520177_1 2.47379446 1 3 4 115 116 38 139 83 68 38 40 0

Total number of rows: 1712

Table truncated, full table size 94 Kbytes.




Supplementary file Size Download File type/resource
GSM307486.gpr.gz 163.7 Kb (ftp)(http) GPR
Processed data included within Sample table
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