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Sample GSM1847066 Query DataSets for GSM1847066
Status Public on Aug 11, 2015
Title Middle-aged 4
Sample type RNA
 
Source name CD11c cells (lungs)
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Lungs
cell type: CD11c cells
cell age: 10-13 months
Extracted molecule total RNA
Extraction protocol Pulmonary CD11 cells separated using magnetic beads (miltenyi). Total RNA from CD11c cells extracted using mirVana kit (Life Technologies) according to manufacturer's protocol. Quality checked using agilent Bioanalyzer.
Label biotin
Label protocol DNA microarray sample processing. RNA sample preparation for hybridization and the subsequent hybridization to the Illumina beadchips were performed at the University of Iowa DNA Facility using the manufacturer’s recommended protocol. Briefly, 100 nanograms total RNA was converted to amplified Biotin- aRNA using the Epicentre TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Illumina, Inc., San Diego, CA, Cat. #TAN07924) according to the manufacturer’s recommended protocol. The amplified Biotin-aRNA product was purified through a QIAGEN RNeasy MinElute Cleanup column (QIAGEN Cat #74204) according to modifications from Epicentre.
 
Hybridization protocol 750 ng of this product were mixed with Illumina hybridization buffer, placed onto Illumina MouseRef-8 v2.0 expression beadchip, and incubated at 58º C for 17h, with rocking, in an Illumina Hybridization Oven. Following hybridization, the arrays were washed, blocked, then stained with streptavidin-Cy3 (Amersham/GE Healthcare, Piscataway, NJ) according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay protocol.
Scan protocol Beadchips were scanned with the Illumina iScan System (ID #N0534) and data were collected using the GenomeStudio software v2011.1.
Description replicate 4
Data processing GenomeStudio software v2011.1.
 
Submission date Aug 10, 2015
Last update date Aug 11, 2015
Contact name Thomas B Bair
E-mail(s) iihg-bioinformatics@uiowa.edu
Organization name University of Iowa
Street address 335 EMRB
City Iowa City
State/province IA
ZIP/Postal code 52242
Country USA
 
Platform ID GPL6885
Series (1)
GSE71868 Gene expression pattern of pulmonary CD11c+ cells from middle-aged and young mice.

Data table header descriptions
ID_REF
VALUE Qunatile normalized
04_A-4.Avg_NBEADS
04_A-4.BEAD_STDERR
04_A-4.Detection Pval

Data table
ID_REF VALUE 04_A-4.Avg_NBEADS 04_A-4.BEAD_STDERR 04_A-4.Detection Pval
ILMN_2896528 927.7188 39 36.30702 0
ILMN_2721178 172.9941 31 11.16643 0
ILMN_3033922 429.9169 43 13.52982 0
ILMN_3092673 2749.413 42 90.72566 0
ILMN_2816356 7.688999 36 2.905736 0.1065163
ILMN_2808939 262.524 28 8.401999 0
ILMN_2634564 227.1912 38 10.26068 0
ILMN_2737647 -2.437486 37 2.370481 0.575188
ILMN_2734484 147.3373 49 9.813871 0
ILMN_2952292 85.62953 55 3.875129 0
ILMN_2699078 -1.133039 40 2.680649 0.4862155
ILMN_1213681 90.99921 42 5.620996 0
ILMN_2735413 1.577853 35 3.301698 0.3070175
ILMN_2735415 -0.5309193 30 2.995195 0.452381
ILMN_2891688 264.7683 36 12.40621 0
ILMN_2637698 803.1285 37 35.64068 0
ILMN_2674228 125.8148 41 6.86622 0
ILMN_2601546 7.389001 29 3.727926 0.1140351
ILMN_1230831 -3.536144 34 2.430696 0.650376
ILMN_2848071 4.135064 28 2.687781 0.1929825

Total number of rows: 25697

Table truncated, full table size 1044 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Raw data are available on Series record

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