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Sample GSM856800 Query DataSets for GSM856800
Status Public on Aug 08, 2012
Title NIH-3T3_Risc-transfected_48h_rep3
Sample type RNA
 
Source name NIH-3T3_Risc-transfected_48h
Organism Mus musculus
Characteristics cell line: NIH-3T3
cell type: murine fibroblast cells
transfectant: RISC-free siRNA (control)
Treatment protocol Cells were transfected with 25nM RNA complexed to DharmaFECT 1 and analysed after 48 hours.
Growth protocol NIH-3T3 fibroblasts were grown in RPMI supplemented with 10% FCS, 2mM L-glutamine, 0.25U/ml penicillin and 100U/ml streptomycin at 37C 5%CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Qiagen miRNeasy kit as described by the manufacturer.
Label biotin
Label protocol Total RNA was converted to cDNA using the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix) and biotinylated using the GeneChip® WT Terminal Labeling Kit (Affymetrix).
 
Hybridization protocol Following fragmentation, 5.5 ug of sscDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip ® Mouse Gene 1.0 ST Array.
Scan protocol GeneChips were scanned using the Agilent Technologies Micro Array Scanner #G2505B.
Description Risc_3
gene expression data from cells transfected with control RNA.
Data processing The data were analyzed with Partek Genomics Suite version 6.5 using Affymetrix default analysis settings and RMA as normalization method. Based on the log 2 value of negative control probes of each chip, the background fluorescence was calculated in StatPlus and used to eliminate the microarray's background noise.
 
Submission date Jan 05, 2012
Last update date Aug 09, 2012
Contact name Dominik Andreas Rückerl
E-mail(s) dominik.ruckerl@manchester.ac.uk
Organization name The University of Manchester
Department Faculty of Biology, Medicine and Health
Street address Oxford Road
City Manchester
ZIP/Postal code M13 9PT
Country United Kingdom
 
Platform ID GPL6246
Series (1)
GSE34873 Experimental identification of miR-378-3p targets by overexpression and silencing in murine NIH-3T3 fibroblasts

Data table header descriptions
ID_REF
VALUE log2 RMA signal intensity

Data table
ID_REF VALUE
10344614 3.87703
10344616 2.92388
10344618 3.11041
10344620 3.19815
10344622 4.55433
10344624 7.62679
10344633 8.74563
10344637 7.42352
10344653 3.19901
10344658 5.61978
10344674 3.20447
10344679 4.44768
10344705 3.43673
10344707 6.18428
10344713 9.30171
10344715 3.3583
10344717 3.69437
10344719 3.95385
10344721 2.96538
10344723 6.15471

Total number of rows: 28853

Table truncated, full table size 475 Kbytes.




Supplementary file Size Download File type/resource
GSM856800_DPM_AB_Risc3_MouseST_220410.CEL.gz 3.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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