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Sample GSM957658 Query DataSets for GSM957658
Status Public on Jul 10, 2012
Title LNCaP-Control-RNAi cells replicate1
Sample type RNA
Source name LNCaP-Control-RNAi cells_replicate1
Organism Homo sapiens
Characteristics cell line: LNCaP
transfection: control-RNAi
Treatment protocol Cells (1 × 10^4) were plated in 100 ul growth medium per well on 96-well plates and incubated overnight. The medium was then changed to growth medium containing hexadimethrine bromide (Sigma) at a final concentration of 8 ug/ml to enhance the transduction efficiency. Lentiviral particles (5-50 ul, 0.5-5 multiplicity of infection) were added and the plates were incubated overnight. Thereafter, we selected stable transductants expressing the shRNAs with puromycin.
Growth protocol Cells were incubated in a humidified atmosphere of 5% CO2 in air at 37°C. RPMI 1640 medium (Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum and antibiotics was used for growth medium. Exponentially growing cells were used for the experiments. Cells were trypsinized, and the number of viable cells was counted by the trypan blue dye-exclusion method.
Extracted molecule total RNA
Extraction protocol Total RNA isolation was performed with a Micro-to-Midi total RNA purification system (Invitrogen). The integrity of total RNAs was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Jul 09, 2012
Last update date Aug 06, 2012
Contact name Yukie Yoshii
Phone 043-206-3429
Organization name National Institute of Radiological Sciences
Street address Anagawa 4-9-1, Inage
City Chiba
ZIP/Postal code 263-8555
Country Japan
Platform ID GPL13607
Series (1)
GSE39183 Characterization of FASN knockdown LNCaP cells

Data table header descriptions
VALUE processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
1 3.885752e+004
2 2.499159e+000
3 2.516892e+000
4 3.666881e+002
5 8.592180e+002
6 3.996927e+001
7 6.436779e+003
8 5.881527e+002
9 2.988092e+004
10 5.223844e+001
11 2.615072e+000
12 1.555046e+003
13 1.168760e+003
14 2.522953e+002
15 8.464265e+003
16 2.643119e+000
17 3.920796e+002
18 2.647903e+000
19 2.649298e+000
20 3.264198e+003

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.

Supplementary file Size Download File type/resource
GSM957658_ControlRNAi_1_AR0685_01raw.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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