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Sample GSM284019 Query DataSets for GSM284019
Status Public on Apr 01, 2010
Title D5-Monocyte - mAdbID:83142
Sample type RNA
 
Channel 1
Source name Monocytes Untreated
Organism Homo sapiens
Characteristics Tissue: blood
Cell type: Monocytes
Extracted molecule total RNA
Extraction protocol RNA extraction with TRIZOL
Extraction method: TRIZOL
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 Sample Labeling Protocol
Other: Small RNA was enriched from 10ug total RNA by flashPAGE (Pre-cast Gel,Type A) (Ambion, Austin, TX, USA) and purified using flashPAGE reaction clean-up kit (Ambion, Austin, TX, USA) according to manufacture’s instruction. The same procedures were applied to obtain small RNA from the Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines that was used as the reference for the miRNA expression array assay. Fragmented small RNA were 3’-end tailed with amine-modified nucleotides and chemically coupled to CyDye fluors (Amersham Biosciences, piscatway, NJ, USA), which sample with Cy5 and the reference with Cy3 respectively, using the mirVana miRNA Labeling Kit (Ambion) following the recommended protocol by the manufactures’ instruction. After labeling, 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).
 
Channel 2
Source name EBV-infected B cell line
Organisms Homo sapiens; human gammaherpesvirus 4
Characteristics Tissue: blood
Cell type: EBV-infected B cell
Extracted molecule total RNA
Extraction protocol RNA extraction with TRIZOL
Extraction method: TRIZOL
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 Sample Labeling Protocol
Other: Small RNA was enriched from 10ug total RNA by flashPAGE (Pre-cast Gel,Type A) (Ambion, Austin, TX, USA) and purified using flashPAGE reaction clean-up kit (Ambion, Austin, TX, USA) according to manufacture~Rs instruction. The same procedures were applied to obtain small RNA from the Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines that was used as the reference for the miRNA expression array assay. Fragmented small RNA were 3~R-end tailed with amine-modified nucleotides and chemically coupled to CyDye fluors (Amersham Biosciences, piscatway, NJ, USA), which sample with Cy5 and the reference with Cy3 respectively, using the mirVana miRNA Labeling Kit (Ambion) following the recommended protocol by the manufactures~R instruction. After labeling, 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).
 
 
Hybridization protocol Sample Hybridization Protocol
Other: Small RNA was enriched from 10ug total RNA by flashPAGE (Pre-cast Gel,Type A) (Ambion, Austin, TX, USA) and purified using flashPAGE reaction clean-up kit (Ambion, Austin, TX, USA) according to manufacture’s instruction. The same procedures were applied to obtain small RNA from the Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines that was used as the reference for the miRNA expression array assay. Fragmented small RNA were 3’-end tailed with amine-modified nucleotides and chemically coupled to CyDye fluors (Amersham Biosciences, piscatway, NJ, USA), which sample with Cy5 and the reference with Cy3 respectively, using the mirVana miRNA Labeling Kit (Ambion) following the recommended protocol by the manufactures’ instruction. After labeling, 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;; 33
LaserPower: 3.18;; 3.4
Temperature: 25.75
Description mAdb experiment ID: 83142
Data processing BRBArrayTools
Calculation Method: Fluorescence intensities generated by Cy5 and Cy3 probes hybridized onto the microarray slides were scanned were scanned on a GenePix 4000 (Axon Instruments, Union City, CA) at variable PMT voltage to obtain maximal signal intensities with < 1% probe saturation. Data were uploaded to National Institute of Health, NCI/CCR µArray database (http://nciarray.nci.nih.gov). Raw data were retrieved in BRB-ArrayTools(http://linus.nci.nih.gov/BRBArrayTools.html) format for analysis and normalization. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 100, and spot size less than 10um 2. genes were filtered out if >80% of experiment with missing data values. 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64. Transcriptional data were process by averaging results in replicate experiments for the same genes. Hierchical clustering analysis was performed on BRBArray tools using centered correlation as similarity metric and centroid linkage method: Cluster 3:0. Heat maps were generated using Eisen’s TreView Software.
 
Submission date Apr 23, 2008
Last update date Mar 23, 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 GPL6773
Series (2)
GSE11248 Peripheral blood stem cell microRNA profiling
GSE11255 Peripheral blood stem cell gene and microRNA profiling

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 -2.134775877 1 1 1 4321 1448 1491 701 13186 5327 2019 710 0
6519905_1 NULL 1 1 2 1582 690 1496 1026 2315 787 2068 792 -50
6519997_1 NULL 1 1 3 1440 571 1526 779 2354 1413 2009 745 -50
6520089_1 NULL 1 1 4 1647 589 1395 683 2283 940 1990 682 -50
6520181_1 -0.734112859 1 1 5 2348 826 1444 584 3433 1105 1994 706 0
6520273_1 0.527197599 1 1 6 2559 730 1519 610 2989 828 1984 662 0
6520365_1 NULL 1 1 7 1759 682 1555 657 2197 772 2053 708 -50
6520385_1 NULL 1 1 8 1726 637 1613 804 2076 702 1996 799 -50
6519885_2 -2.134775877 1 2 1 4041 1561 1582 725 12828 5450 2079 761 0
6519905_2 NULL 1 2 2 1429 611 1586 837 2048 811 2086 846 -50
6519997_2 NULL 1 2 3 1522 635 1494 607 2283 681 2052 721 -50
6520089_2 NULL 1 2 4 1663 583 1494 574 2126 845 2014 740 -50
6520181_2 -0.734112859 1 2 5 2527 966 1515 1135 3331 1083 2065 759 0
6520273_2 0.527197599 1 2 6 2650 762 1584 679 2528 720 2117 885 0
6520365_2 NULL 1 2 7 1777 643 1639 601 2020 711 2030 765 -50
6520385_2 NULL 1 2 8 1592 626 1603 584 2178 817 2095 722 -50
6519889_1 0.517833114 1 3 1 7844 2621 1620 1256 6351 2105 2069 684 0
6519981_1 -0.614975035 1 3 2 3578 845 1566 561 4975 1260 2058 1159 0
6520001_1 NULL 1 3 3 1614 647 1601 739 2139 808 2038 716 -50
6520093_1 NULL 1 3 4 1635 679 1637 623 2273 674 2116 716 -50

Total number of rows: 1456

Table truncated, full table size 90 Kbytes.




Supplementary file Size Download File type/resource
GSM284019.gpr.gz 136.9 Kb (ftp)(http) GPR
Processed data included within Sample table

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