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Sample GSM1847064 Query DataSets for GSM1847064
Status Public on Aug 11, 2015
Title Middle-aged 2
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 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
02_A-2.Avg_NBEADS
02_A-2.BEAD_STDERR
02_A-2.Detection Pval

Data table
ID_REF VALUE 02_A-2.Avg_NBEADS 02_A-2.BEAD_STDERR 02_A-2.Detection Pval
ILMN_2896528 923.9254 43 62.6601 0
ILMN_2721178 174.7437 34 15.88965 0
ILMN_3033922 471.9522 60 34.45909 0
ILMN_3092673 2749.413 56 155.8109 0
ILMN_2816356 10.68538 49 3.850458 0.06140351
ILMN_2808939 261.6449 44 24.97692 0
ILMN_2634564 205.0069 45 17.38188 0
ILMN_2737647 -3.322257 31 3.944699 0.6691729
ILMN_2734484 168.1763 49 15.75724 0
ILMN_2952292 86.09113 46 10.11327 0
ILMN_2699078 -4.716908 43 2.832126 0.7731829
ILMN_1213681 78.87168 40 9.652495 0
ILMN_2735413 13.06748 31 5.222985 0.04761905
ILMN_2735415 10.58515 41 4.468193 0.06265664
ILMN_2891688 243.4884 37 25.56131 0
ILMN_2637698 918.0908 44 74.64821 0
ILMN_2674228 125.1796 51 12.32592 0
ILMN_2601546 11.99512 38 5.536066 0.04887218
ILMN_1230831 -2.481232 23 5.940203 0.6027569
ILMN_2848071 6.884788 36 4.198267 0.1215539

Total number of rows: 25697

Table truncated, full table size 1041 Kbytes.




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

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