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Sample GSM284007 Query DataSets for GSM284007
Status Public on Apr 01, 2010
Title D1-T cell - mAdbID:83122
Sample type RNA
 
Channel 1
Source name T cell Untreated
Organism Homo sapiens
Characteristics Tissue: blood
Cell type: T 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 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: 3.23;; 3.57
Temperature: 28.68
Description mAdb experiment ID: 83122
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 -2.456313372 1 1 1 8795 3085 2952 1440 31719 10671 2963 875 0
6519905_1 NULL 1 1 2 3266 1353 3174 1540 2772 780 2945 830 -50
6519997_1 -1.172914863 1 1 3 3464 1645 3285 1199 3566 1493 3050 796 -50
6520089_1 NULL 1 1 4 3468 1488 3218 1176 3225 1530 3004 1659 -50
6520181_1 -1.122160196 1 1 5 4995 1522 3127 1123 5706 1694 2950 851 0
6520273_1 1.155041814 1 1 6 4900 5357 3351 1026 3259 657 3070 759 0
6520365_1 NULL 1 1 7 3307 1006 3394 1032 3221 1113 3023 830 -50
6520385_1 NULL 1 1 8 3921 2449 3290 1585 3316 1562 3048 926 -50
6519885_2 -2.456313372 1 2 1 8957 2519 3027 1990 32056 10769 2813 722 0
6519905_2 NULL 1 2 2 2994 1047 3189 1377 2900 635 2949 876 -50
6519997_2 -1.172914863 1 2 3 5952 2021 3341 960 6519 2795 2990 692 0
6520089_2 NULL 1 2 4 3232 1034 3255 1017 2974 722 2988 868 -50
6520181_2 -1.122160196 1 2 5 6317 3417 3186 2292 6205 3048 3053 769 0
6520273_2 1.155041814 1 2 6 3607 1009 3393 1077 2979 943 3079 883 -50
6520365_2 NULL 1 2 7 3036 913 3395 2011 3058 1541 3051 777 -50
6520385_2 NULL 1 2 8 3946 2603 3443 1116 3409 1777 3096 774 -50
6519889_1 0.231387421 1 3 1 8748 2862 2950 977 6479 2526 2812 778 0
6519981_1 -0.963662803 1 3 2 6618 1402 3087 1041 7792 1586 2905 926 0
6520001_1 NULL 1 3 3 3466 1184 3188 1524 3088 1148 2964 1433 -50
6520093_1 NULL 1 3 4 3238 898 3224 1401 2802 831 2915 2440 -50

Total number of rows: 1456

Table truncated, full table size 92 Kbytes.




Supplementary file Size Download File type/resource
GSM284007.gpr.gz 141.0 Kb (ftp)(http) GPR
Processed data included within Sample table

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