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Sample GSM820717 Query DataSets for GSM820717
Status Public on Oct 22, 2011
Title intermediate_mature_bone_marrowMCs_and_MMs_AO.B2
Sample type RNA
 
Source name Bone marrow neutrophil precursors
Organism Homo sapiens
Characteristics maturation stage: myelocytes and metamyelocytes
Extracted molecule total RNA
Extraction protocol All cell populations were isolated on a PercollTM density gradient followed by immunomagnetic depletion as described in Bjerregaard MD, Jurlander J, Klausen P, Borregaard N, Cowland JB: The in vivo profile of transcription factors during neutrophil differentiation in human bone marrow. Blood 2003, 101: 4322-4332.
Label Hy5
Label protocol Total RNA extracted from BM and PB cell populations was labeled with the miRCURYTM Array Labeling kit (Exiqon, Vedbæk, Denmark) and hybridized to miRCURYTM LNA microRNA Arrays (Exiqon) in a Tecan HS400 hybridization station (Tecan Nordic AB, Brøndby, Denmark). Labeling with the fluorescent dyes Hy3 and Hy5 and preparation of wash buffers were done according to the manufacturer’s instructions (Exiqon)
 
Hybridization protocol Slides were placed in the hybridization chambers and primed by injecting hybridization buffer into each chamber. Finally, the target preparations were injected and incubated for 16 hours at 60ºC with medium agitation. After hybridization, slides were washed, soaked in wash buffers, and dried as recommended by the manufacturer (Exiqon). Slides were removed from the hybridization station and kept in the dark in a nitrogen sphere until scanning.
Scan protocol Slides were scanned in an Agilent DNA microarray scanner (G2565BA). Image analysis was performed using the Genepix® Pro Software (version 6.1.2; Molecular Devices, Philadelphia, USA). A gene array list(GAL) file (www.exiqon.com. GAL file: 208000V8.1_208001V8.1_208002V8.1_lot_number_20278-20399_hsap.gal. 2-11-2007) with miRNA annotations according to miRBase (version 10) was applied to annotate features and generate a Genepix Results (GPR) File for each image, with median foreground and mean background values for each spot.
Description US22502610_13638666_S01_Cropped_001.gpr
numbers = person; letters = cell population
Biological replicate 3b
Data processing GPR files were loaded into the R (version 2.0.1) software environment (Gentleman R, Isaka R: R: A Language for Data Analysis and Graphics. Journal of Computational and Graphical Statistics 1996, 5: 299-314) using the Limma software package (Smyth, G. K. (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397–420). Normalization of fluorescence signals between all samples was performed in R (version 2.0.1) using qspline (Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielser HB et al.: A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol 2002, 3(9):research0048) prior to all statistical analysis.
 
Submission date Oct 21, 2011
Last update date Oct 22, 2011
Contact name Corinna Cavan Pedersen
E-mail(s) corinnacp@yahoo.com
Organization name Rigshospitalet
Street address Juliane Mariesvej 20, 9322
City Copenhagen
ZIP/Postal code 2100
Country Denmark
 
Platform ID GPL13273
Series (1)
GSE33140 Human bone marrow precursor cells

Data table header descriptions
ID_REF
VALUE qspline normalized fluorescence intensities sorted according to increasing p-values as calculated in a one-way ANOVA performed to identify differentially expressed miRNA genes between the bone marrow and peripheral blood cell populations from the 4 donors

Data table
ID_REF VALUE
2 83.08
3 106.25
4 183.28
5 83.08
6 78.61
7 70.48
8 62.21
9 68.17
10 67.25
11 103.02
12 74.60
13 84.28
15 98.28
16 116.85
17 138.56
18 369.27
19 67.25
20 106.92
21 69.73
22 80.18

Total number of rows: 6240

Table truncated, full table size 68 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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