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Sample GSM1847065 Query DataSets for GSM1847065
Status Public on Aug 11, 2015
Title Middle-aged 3
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 3
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
03_A-3.Avg_NBEADS
03_A-3.BEAD_STDERR
03_A-3.Detection Pval

Data table
ID_REF VALUE 03_A-3.Avg_NBEADS 03_A-3.BEAD_STDERR 03_A-3.Detection Pval
ILMN_2896528 916.3305 37 22.73446 0
ILMN_2721178 184.7114 38 6.310596 0
ILMN_3033922 369.0706 44 11.54191 0
ILMN_3092673 2630.422 41 52.37631 0
ILMN_2816356 2.661887 39 2.043869 0.2669173
ILMN_2808939 241.0555 43 7.798774 0
ILMN_2634564 211.6793 23 16.73017 0
ILMN_2737647 -2.890532 27 2.296508 0.6353384
ILMN_2734484 136.4941 51 6.545249 0
ILMN_2952292 97.54082 45 3.8818 0
ILMN_2699078 0.8995388 42 2.930556 0.3546366
ILMN_1213681 79.25256 43 5.052904 0
ILMN_2735413 4.232859 36 2.733491 0.2067669
ILMN_2735415 -7.241226 25 2.020533 0.9110276
ILMN_2891688 222.089 40 8.407758 0
ILMN_2637698 837.8182 48 20.54272 0
ILMN_2674228 136.6295 35 6.473573 0
ILMN_2601546 20.27427 47 4.481467 0.01378446
ILMN_1230831 -10.26074 29 1.912359 0.9849624
ILMN_2848071 5.074414 37 2.821397 0.1779449

Total number of rows: 25697

Table truncated, full table size 1035 Kbytes.




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

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