NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1054123 Query DataSets for GSM1054123
Status Public on Dec 18, 2012
Title Mouse_pancreatic_aTC1-6, cytokines, 48H (rep 2)
Sample type RNA
 
Source name Mouse pancreatic glucagonoma cell line aTC1-6, Cytokines, 48H
Organism Mus musculus
Characteristics cell type: Pancreatic alpha cell
activation agent: Cytokines
time: 48H
cell line: aTC1-6
treatment: IL1b 50 IU/ml; IFNg 1000 IU/ml; TNFa 1000 IU/ml
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 Test
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 0.14576942
2 0.209410836
3 0.115168893
4 0.210307178
5 0.084453616
6 0.105984339
7 2.43652E-05
8 0.000148775
9 0.110268146
10 0.103853662
11 31.77070062
12 28.07023039
13 0.420606777
14 1.94828E-07
15 0.19148828
16 0.025165935
17 0.140738505
18 0.824912498
19 1.94828E-07
20 5.22125E-05

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap