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Sample GSM173158 Query DataSets for GSM173158
Status Public on Jun 17, 2007
Title hsa_T-cell-CD4-A301 vs. synthetic miRNA pool rep1
Sample type RNA
 
Channel 1
Source name synthetic miRNA pool
Organism synthetic construct
Characteristics 5 fmol of each of 816 synthetic miRNAs were pooled and labelled.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted as described in: Pfeffer, S., Lagos-Quintana, M., and Tuschl, T. (2003). Cloning of small RNA molecules. In Current Protocols in Molecular Biology, F. M. Ausubel, R. Brent, R. E. Kingston , D. D. Moore, J. G. Seidmann, J. A. Smith, and K. Struhl, eds. (New York, John Wiley and Sons), pp. 26.24.21-26.24.18.
Label Hy3
Label protocol 5 µg total RNA was labelled using a commercial kit (miRCuryTM LNA microRNA Array labeling kit, Exiqon) following the instructions of the manufacturer
 
Channel 2
Source name hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD4
Organism Homo sapiens
Characteristics CD4+ T-cell line provided by F.A. Grässer, graesser@med-rz.uni-sb.de
Extracted molecule total RNA
Extraction protocol Total RNA was extracted as described in: Pfeffer, S., Lagos-Quintana, M., and Tuschl, T. (2003). Cloning of small RNA molecules. In Current Protocols in Molecular Biology, F. M. Ausubel, R. Brent, R. E. Kingston , D. D. Moore, J. G. Seidmann, J. A. Smith, and K. Struhl, eds. (New York, John Wiley and Sons), pp. 26.24.21-26.24.18.
Label Hy5
Label protocol 5 µg total RNA was labelled using a commercial kit (miRCuryTM LNA microRNA Array labeling kit, Exiqon) following the instructions of the manufacturer
 
 
Hybridization protocol 5 µg of respective total RNA were mixed with 2.5 fmol of each of four RNA oligonucleotides reverse complement to miRControl 1 probes and 5 fmol of each of 20 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled by 3’ ligation. Total RNA mix was hybridized in a dual colour approach to microarrays versus a second labelled synthetic miRNA pool. The sy
Scan protocol Image capture was done with Agilent DNA-Microarray Scanner (Agilent, Santa Clara, CA)
Description PMID
Data processing Signal processing and quantification was done with ImaGene software version 5.0 (BioDiscovery, Los Angeles, CA). For each spot, the local signal was measured inside a fixed circle of 230-280 µm diameter, and background was measured outside the circle within specified rings 30 µm distant to the signal and 100 µm wide. Signal and background was taken to be the average of pixels between defined low and high percentages of maximum intensity with percentage parameter settings for low/high being 2/97% for signal and 0/97% for background. Local background was subtracted from the signal to obtain the net signal intensity and the ratio of both fluorescent labels. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots) and for which the fluorescent intensity in of the miRNAs derived from the samples of interest was two-fold the mean background value (2bkg dataset). The mean ratios of all probes were normalized to the median of the ratios detected for the spiked 20 synthetic RNA oligonucleotides reverse complement to miRControl 3 probes.
 
Submission date Mar 06, 2007
Last update date Mar 23, 2007
Contact name Frank Huebel
E-mail(s) frank.huebel@miltenyibiotec.de
Fax +49 221 950 48 48
URL http://www.miltenyibiotec.com
Organization name Miltenyi Biotec GmbH, MACS Molecular Business Unit
Department MACS Molecular 9
Street address Stoeckheimer Weg 1
City COLOGNE
State/province NRW
ZIP/Postal code 50829
Country Germany
 
Platform ID GPL4867
Series (1)
GSE7233 A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing

Data table header descriptions
ID_REF
VALUE normalized log2 ratio defined as Ch2/Ch1 (valid data of up to n reps used only)

Data table
ID_REF VALUE
1 -4.3196
2 -3.6051
3
4
5
6 -4.7049
7 -3.5545
8
9
10
11
12
13
14 -3.3508
15
16 -6.4937
17
18
19 -0.8661
20 -0.8794

Total number of rows: 885

Table truncated, full table size 4 Kbytes.




Supplementary file Size Download File type/resource
GSM173158.txt.gz 74.2 Kb (ftp)(http) TXT

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