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Sample GSM284028 Query DataSets for GSM284028
Status Public on Apr 01, 2010
Title D3-NK cell - mAdbID:83157
Sample type RNA
 
Channel 1
Source name NK cell Untreated
Organism Homo sapiens
Characteristics Tissue: blood
Cell type: NK 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: 100;; 100
LaserPower: 3.43;; 3.6
Temperature: 32.37
Description mAdb experiment ID: 83157
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 -3.663974285 1 1 1 4416 1184 2119 457 52521 14304 2852 483 0
6519905_1 NULL 1 1 2 2077 412 2112 501 2963 455 2562 527 -50
6519997_1 NULL 1 1 3 2241 446 2075 459 2472 432 2366 461 -50
6520089_1 NULL 1 1 4 2436 498 2052 444 2655 415 2319 408 -50
6520181_1 -2.581991673 1 1 5 2942 569 2038 433 6207 1277 2345 394 0
6520273_1 0.431834847 1 1 6 3611 605 2020 480 2874 476 2313 398 0
6520365_1 NULL 1 1 7 2307 592 1939 435 2288 448 2333 401 -50
6520385_1 NULL 1 1 8 2090 421 2004 468 2216 432 2338 407 -50
6519885_2 -3.663974285 1 2 1 4706 1063 2110 476 53358 11507 2627 559 0
6519905_2 NULL 1 2 2 2161 525 2108 514 2339 426 2264 412 -50
6519997_2 NULL 1 2 3 2057 492 2064 522 2238 410 2286 466 -50
6520089_2 NULL 1 2 4 2400 504 2084 436 2372 373 2349 427 -50
6520181_2 -2.581991673 1 2 5 3166 651 2154 546 6257 1291 2311 687 0
6520273_2 0.431834847 1 2 6 3449 553 2012 459 2560 431 2289 443 0
6520365_2 NULL 1 2 7 2169 525 1910 431 2319 384 2269 394 -50
6520385_2 NULL 1 2 8 1973 509 1962 430 2281 360 2335 414 -50
6519889_1 1.138694763 1 3 1 9974 1972 2004 474 6957 1300 2388 465 0
6519981_1 -2.259733677 1 3 2 3817 561 2079 483 9406 1129 2287 389 0
6520001_1 NULL 1 3 3 2265 512 2039 424 2034 372 2189 400 -50
6520093_1 NULL 1 3 4 2313 511 2008 452 2222 453 2177 382 -50

Total number of rows: 1456

Table truncated, full table size 91 Kbytes.




Supplementary file Size Download File type/resource
GSM284028.gpr.gz 137.6 Kb (ftp)(http) GPR
Processed data included within Sample table

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