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Status |
Public on Jan 01, 2011 |
Title |
MMC_rep1 |
Sample type |
RNA |
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Source name |
mucosal-type mast cells
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Organism |
Mus musculus |
Characteristics |
strain: Balb/c group: MMC
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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.
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Growth protocol |
Culture of bone marrow cells in complete RPMI 1640 supplemented with IL3 (5ng/ml) and SCF (20ng/ml) for 4 weeks.
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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.
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Label |
Cy3
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Label protocol |
Standard Agilent labeling protocol with 100 ng quality-checked total RNA.
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Hybridization protocol |
Standard Agilent labeling protocol: the labeled samples were hybridized for 20 hours at 55°C.
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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).
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Description |
microRNA profiling of mucosal-type mast cells generated by additional differentiation of immature BMMCs for 5 days by supplementation of IL9 and TGFbeta.
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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.
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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 |
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Platform ID |
GPL8824 |
Series (1) |
GSE24321 |
MicroRNA profiling of mouse bone marrow-derived mast cells during mucosal differentiation and IgE-mediated activation |
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