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Sample GSM1847070 Query DataSets for GSM1847070
Status Public on Aug 11, 2015
Title Young 4
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 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
08_Y-4.Avg_NBEADS
08_Y-4.BEAD_STDERR
08_Y-4.Detection Pval

Data table
ID_REF VALUE 08_Y-4.Avg_NBEADS 08_Y-4.BEAD_STDERR 08_Y-4.Detection Pval
ILMN_2896528 943.4704 32 62.37045 0
ILMN_2721178 217.9973 47 15.41475 0
ILMN_3033922 418.3967 51 25.79885 0
ILMN_3092673 2761.473 40 147.7643 0
ILMN_2816356 8.369171 27 4.909513 0.09649123
ILMN_2808939 238.5072 36 20.75107 0
ILMN_2634564 255.4591 37 17.23598 0
ILMN_2737647 -3.863392 32 4.204467 0.7117795
ILMN_2734484 146.3035 33 16.06989 0
ILMN_2952292 111.0563 50 7.707259 0
ILMN_2699078 -1.657519 35 2.80982 0.5488722
ILMN_1213681 88.76659 46 6.907585 0
ILMN_2735413 -1.870954 36 2.436307 0.575188
ILMN_2735415 7.49619 33 5.371106 0.1177945
ILMN_2891688 264.4327 41 18.77477 0
ILMN_2637698 812.0804 54 44.5225 0
ILMN_2674228 205.4218 42 14.19535 0
ILMN_2601546 8.597154 45 3.391067 0.0952381
ILMN_1230831 -4.339048 34 3.765602 0.7393484
ILMN_2848071 3.865098 27 3.675319 0.2230576

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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