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Sample GSM1847068 Query DataSets for GSM1847068
Status Public on Aug 11, 2015
Title Young 2
Sample type RNA
 
Source name CD11c cells (lungs)
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Lungs
cell type: CD11c cells
cell age: 6-8 weeks
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 2
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
06_Y-2.Avg_NBEADS
06_Y-2.BEAD_STDERR
06_Y-2.Detection Pval

Data table
ID_REF VALUE 06_Y-2.Avg_NBEADS 06_Y-2.BEAD_STDERR 06_Y-2.Detection Pval
ILMN_2896528 967.7332 43 35.38176 0
ILMN_2721178 214.1457 46 8.077449 0
ILMN_3033922 491.295 38 15.3566 0
ILMN_3092673 2455.683 35 86.43995 0
ILMN_2816356 14.07054 30 4.947792 0.03884712
ILMN_2808939 246.2787 46 12.76842 0
ILMN_2634564 219.3438 49 11.44001 0
ILMN_2737647 -3.022366 34 2.866802 0.660401
ILMN_2734484 141.8983 41 10.24477 0
ILMN_2952292 75.85152 50 4.122382 0
ILMN_2699078 -6.01633 51 2.193803 0.8508772
ILMN_1213681 95.92529 56 4.453749 0
ILMN_2735413 -1.209771 46 2.609498 0.5350877
ILMN_2735415 0.7931345 35 3.30359 0.3822055
ILMN_2891688 253.3255 42 10.60411 0
ILMN_2637698 784.9808 51 26.42705 0
ILMN_2674228 216.4301 43 10.73927 0
ILMN_2601546 4.31427 33 2.425237 0.2230576
ILMN_1230831 5.103255 44 3.46091 0.1929825
ILMN_2848071 10.80666 32 3.800769 0.07393484

Total number of rows: 25697

Table truncated, full table size 1038 Kbytes.




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

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