Mark Fellmann, Div. Of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
Treatment protocol
chemically synthesized siRNAs (Qiagen, Hilden, Germany) were transfected with HiPerFect (Qiagen, Hilden, Germany) according to standard transfection procedure
Growth protocol
cells were cultivated in Minimum Essential Media (1x) (MEM, Invitrogen, Grand Island, NY, USA), supplemented with 10 % fetal calf serum (FCS), 50 U/ml penicillin, and 50 ?g/ml streptomycin sulfate, 1% non-essential amino acids (Invitrogen, Grand Island, NY, USA) and 100 ?g/ml insulin bovine
Extracted molecule
total RNA
Extraction protocol
total RNA was extracted using Rneasy mini-prep kit (Qiagen, Hilden, Germany; 2?g total RNA was amplified one round based on T7 RNA Polymerase (Agilent low RNA Input Amplification Kit)
Label
Cy3
Label protocol
direct fluorescent labelling of 2 ?g amplified RNA, anneling of 0.5?g Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42?C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy3-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy3-labeled probes were purified with Microcon YM-30 column
Mark Fellmann, Div. Of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
Treatment protocol
chemically synthesized siRNAs (Qiagen, Hilden, Germany) were transfected with HiPerFect (Qiagen, Hilden, Germany) according to standard transfection procedure
Growth protocol
cells were cultivated in Minimum Essential Media (1x) (MEM, Invitrogen, Grand Island, NY, USA), supplemented with 10 % fetal calf serum (FCS), 50 U/ml penicillin, and 50 ?g/ml streptomycin sulfate, 1% non-essential amino acids (Invitrogen, Grand Island, NY, USA) and 100 ?g/ml insulin bovine
Extracted molecule
total RNA
Extraction protocol
total RNA was extracted using Rneasy mini-prep kit (Qiagen, Hilden, Germany; 2?g total RNA was amplified one round based on T7 RNA Polymerase (Agilent low RNA Input Amplification Kit)
Label
Cy5
Label protocol
direct fluorescent labelling of 2 ?g amplified RNA, anneling of 0.5?g Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42?C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy5-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy5-labeled probes were purified with Microcon YM-30 column
Hybridization protocol
ch1 and ch2 together are solved in 50 ?l 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x DenhardtÆs solution and 2 ng/?l Cot1-DNA (Invitrogen); sample was denaturated at 65?C for 2min, hybridzation of arrays were performed in Corning chambers 14h at 37?C; slides were washed twice in 1xSSC+0.1SDS and once in 0.1xSSC+ 0.1SDS before air pressure drying and scanning
Scan protocol
arrays were scanned with the GenePix 4000B microarray scanner and analyzed using GenePix Pro 4.1 software (Axon Instruments)
Description
MCF7 ESRalpha positive breast cancer cell line, siRNA mediadet knock-down FOXA1 siRNA_FOXA1_DKFZ_Replicate1_dyeswap
Data processing
raw data processing was performed using ArrayMagic (Buness et al., 2005) including VSN normalization method; after removal of bad quality clones, generalized log ratios from 26629 cDNA clones were given in the data table
