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Sample GSM1054119 Query DataSets for GSM1054119
Status Public on Dec 18, 2012
Title Mouse_pancreatic_aTC1-6, control, 48H (rep 1)
Sample type RNA
 
Source name Mouse pancreatic glucagonoma cell line aTC1-6, Control, 48H
Organism Mus musculus
Characteristics cell type: Pancreatic alpha cell
activation agent: Control
time: 48H
cell line: aTC1-6
treatment: control
Treatment protocol αTC1-6 and βTC1 cells (passages 20-40) were seeded the day before treatment in 60 mm dishes at a density of 4.5 x 10e5 cells. Control cells were grown without any treatment; test cells were treated with a cocktail of inflammatory cytokines containing IL1b 50 IU/ml; IFNg 1000 IU/ml; TNFa 1000 IU/ml
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol (Lifetechnologies™, Foster-City, CA, USA), according to manufacturer's instructions.
Label FAM
Label protocol PCR assays were performed using TaqMan® Rodent miRNA A+B Cards Set v2.0. Specifically RNA for HT miRNA expression profiling was reverse transcribed into cDNA of 519 mouse-specific and 68 rat-specific miRNAs through Megaplex™ RT Rodent Primer Pool sets, and preamplified through Megaplex™ PreAmp Rodent Primer Pool sets (Lifetechnologies™). Resulting cDNAs were loaded onto TaqMan Low Density miR Arrays (TLDA) cards, according to manufacturer’s instructions.
 
Hybridization protocol n/a
Scan protocol n/a
Description Control
Data processing Matrix non-normalized worksheet reports non-normalized Ct values as obtained through RQ Manager v. 1.2 (Applied Biosystems), starting from .sds files.
The normalization and all the data analysis were performed trough Real-Time Statminer© software (www.integromics.com) (Integromics, Granada, Spain). Multiple reference genes were used to normalise data: Genorm (integrated into Real-Time Statminer©) and DataAssist™ (Lifetechnologies™) software allowed to choose the best ones.
Target gene signals normalized to housekeeping genes; Data are reported as DCt = (Ct_Target − Ct_HKG)] and 2^-DCt
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports as test/control (e.g., Cytokines treated/Control cells or bTC1 Control/aTC1 Control) ratios.
 
Submission date Dec 17, 2012
Last update date Dec 18, 2012
Contact name Michele Purrello
E-mail(s) purrello@unict.it, dbarbaga@unict.it
Organization name University of Catania
Street address Via S. Sofia, 87
City Catania
ZIP/Postal code 95123
Country Italy
 
Platform ID GPL11199
Series (1)
GSE42970 Global microRNA profiling of aTC1-6 and bTC1 before and after treatment with cytokines

Data table header descriptions
ID_REF
VALUE 2^-DCt normalized to housekeeping genes

Data table
ID_REF VALUE
1 0.498715864
2
3 0.254378915
4 0.97436688
5 0.126527422
6 0.254393727
7
8 0.000106366
9 0.161203503
10 0.061774447
11 37.70199603
12 39.08079743
13 1.019094614
14 0.002491078
15 4.69388E-07
16 0.061892225
17 0.254017536
18 0.998435406
19 4.69388E-07
20 2493.342745

Total number of rows: 768

Table truncated, full table size 11 Kbytes.




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

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