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Sample GSM599745 Query DataSets for GSM599745
Status Public on Jan 01, 2011
Title MMC_rep1
Sample type RNA
 
Source name mucosal-type mast cells
Organism Mus musculus
Characteristics strain: Balb/c
group: MMC
Treatment protocol Bone marrow-derived mouse mast cells (BMMCs) were cultured for 4 weeks in the presence of SCF and IL-3. On the 6th day, CD117+ cells (putative committed immature progenitors) were magnetically separated. In order to differentiate the 4 weeks old BMMCs toward mucosal-type mast cells the medium was supplemented with IL-9+TGF-beta for 5 additional days. BMMCs were activated by IgE-crosslinking.
Growth protocol Culture of bone marrow cells in complete RPMI 1640 supplemented with IL3 (5ng/ml) and SCF (20ng/ml) for 4 weeks.
Extracted molecule total RNA
Extraction protocol RNAs from cell samples was extracted by miRNeasy Mini Kit, the quantity and quality of total RNA was assessed by NanoDrop ND-1000 spectrophotometer and Agilent 2100 Bioanalyzer, respectively. Only those samples were used for microarray experiments that gave >8.0 for RNA integrity number, showed a clear gel image and no DNA contamination was observed on the histogram.
Label Cy3
Label protocol Standard Agilent labeling protocol with 100 ng quality-checked total RNA.
 
Hybridization protocol Standard Agilent labeling protocol: the labeled samples were hybridized for 20 hours at 55°C.
Scan protocol Standard Agilent labeling protocol: the arrays were scanned with an Agilent DNA Microarray Scanner BA. The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol miRNA-v1_95_May07 and grid: 019119_D_20080215).
Description microRNA profiling of mucosal-type mast cells generated by additional differentiation of immature BMMCs for 5 days by supplementation of IL9 and TGFbeta.
Data processing Extracted data were analyzed by Genespring GX10.0. Raw data were normalized to the 75th percentile signal intensity and entities showing present call in all samples of a condition were filtered out. Differentially expressed genes were selected when passing the signal intensity filter (entities where at least 100 percent of samples in any 1 out of 4 conditions have values within cut-off) and showing at least 2-fold statistically significant change (ANOVA and Tukey HSD post-hoc test, with Benjamini-Hochberg Multiple Testing Correction p-value<0,05) between BMMC and any other groups.
 
Submission date Sep 23, 2010
Last update date Jan 01, 2011
Contact name Viktor Molnár
E-mail(s) molvik.dgci@gmail.com
Organization name Semmelweis University
Department Department of Genetics, Cell- and Immunobiology
Street address Nagyvárad tér 4.
City Budapest
ZIP/Postal code 1089
Country Hungary
 
Platform ID GPL8824
Series (1)
GSE24321 MicroRNA profiling of mouse bone marrow-derived mast cells during mucosal differentiation and IgE-mediated activation

Data table header descriptions
ID_REF
VALUE 75th percentile normalized, per gene median centralized log2 signal intensities

Data table
ID_REF VALUE
DarkCorner -0.17875218
NC1_00000197 -1.4645574
NC1_00000215 -0.5698148
NC2_00079215 -0.6691499
NC2_00092197 -1.0512242
NC2_00106057 -0.3227657
NC2_00122731 -0.4759264
NegativeControl -0.33119738
SCorner3 -0.25419044
dmr_285 -0.5592818
dmr_3 -0.25419044
dmr_308 -0.25419044
dmr_316 -0.31241846
dmr_31a -0.25419044
dmr_6 -0.69408226
hur_1 -0.55508757
hur_2 -0.35892487
hur_4 -0.3882165
hur_5 -0.25419044
hur_6 -0.99966335

Total number of rows: 599

Table truncated, full table size 14 Kbytes.




Supplementary file Size Download File type/resource
GSM599745.txt.gz 1.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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