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Sample GSM1847063 Query DataSets for GSM1847063
Status Public on Aug 11, 2015
Title Middle-aged 1
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 1
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
01_A-1.Avg_NBEADS
01_A-1.BEAD_STDERR
01_A-1.Detection Pval

Data table
ID_REF VALUE 01_A-1.Avg_NBEADS 01_A-1.BEAD_STDERR 01_A-1.Detection Pval
ILMN_2896528 980.689 44 29.95038 0
ILMN_2721178 178.196 40 8.150301 0
ILMN_3033922 441.297 48 17.09107 0
ILMN_3092673 2451.734 46 75.02997 0
ILMN_2816356 14.82637 41 4.085742 0.03258145
ILMN_2808939 250.3001 30 13.74697 0
ILMN_2634564 190.4897 38 15.13267 0
ILMN_2737647 2.722074 25 4.146051 0.2932331
ILMN_2734484 151.8677 42 8.999267 0
ILMN_2952292 97.20732 56 4.88358 0
ILMN_2699078 -7.503572 41 2.595203 0.8934837
ILMN_1213681 70.22035 46 5.133772 0
ILMN_2735413 9.561045 35 4.794399 0.0839599
ILMN_2735415 9.777976 37 4.113903 0.0802005
ILMN_2891688 306.5565 41 15.04373 0
ILMN_2637698 807.707 44 28.81772 0
ILMN_2674228 146.4606 35 7.828989 0
ILMN_2601546 5.02856 43 3.120401 0.1817043
ILMN_1230831 -3.076326 37 3.065902 0.6516291
ILMN_2848071 10.64141 40 3.544254 0.0651629

Total number of rows: 25697

Table truncated, full table size 1031 Kbytes.




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

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