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Sample GSM940692 Query DataSets for GSM940692
Status Public on May 31, 2015
Title siLCN2_1
Sample type RNA
 
Source name MDA-MB-231 siLCN2
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
transfection: siRNA LCN2
Growth protocol siRNA LCN2 tranfected MDA-MB-231 breast cancer cells were grown in DMEM low glucose + 10%SVF
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at technical platform of the IUH (Paris).
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description This sample is of siLCN2 MDA-MB-231. It is the first of three sicontrol biological replicates used in this experiment, each from separate cultures.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date May 31, 2012
Last update date May 31, 2015
Contact name Pierre de la Grange
E-mail(s) [email protected]
Organization name GenoSplice technology
Department Paris Biotech Santé
Street address 29, rue du Faubourg Saint-Jacques
City Paris
ZIP/Postal code 75014
Country France
 
Platform ID GPL11219
Series (1)
GSE38369 Lipocalin 2 (LCN2), the TNF-like receptor TWEAKR and its ligand TWEAK act downstream of NFAT1 to regulate breast cancer cell invasion

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AB000409 511.98
AB000461 4408.12
AB000463 526.68
AB000781 12.04
AB001025 119.44
AB001328 10.50
AB002294 1914.27
AB002308 3761.09
AB002311 1196.07
AB002313 6445.88
AB002360 16.39
AB002372 337.51
AB002377 1283.08
AB002381 1275.89
AB002382 14114.00
AB002384 5.96
AB003177 2244.72
AB003333 8644.16
AB004885 424.92
AB006589 36.63

Total number of rows: 47633

Table truncated, full table size 774 Kbytes.




Supplementary file Size Download File type/resource
GSM940692_45815302_532.pair.gz 6.0 Mb (ftp)(http) PAIR
Processed data included within Sample table

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