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Sample GSM2391665 Query DataSets for GSM2391665
Status Public on Nov 16, 2016
Title SCC13 cells control replicate_LPS 4
Sample type RNA
Source name control LPS
Organism Homo sapiens
Characteristics cell line: SCC13
transfection agent: pUNO
treatment: LPS 10μg/ml replicate 4
Treatment protocol SCC13 tumor cells were stably transfected with control (pUNO, Invivogen) and TLR4 expressing plasmid (pUNO-TLR4GFP, Invivogen) following the manufacturer’s protocol. For the selection of positive clones the transfected cells were further grown in DMEM medium containing blasticidine (10μg/ml) as a selection marker. Afterwards cells were treated with 10μg/ml ultrapure LPS (Sigma) for 24 hours.
Growth protocol SCC13 cell lines were grown in conventional DMEM medium supplied with 10% fetal calf serum
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol (Invitrogen) according to manufacturer's protocol
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).Quantification and and quality assessment were done using Nanodrop spectrophotometer (Witec) and Agilent 2100 Bioanalyzer (Agilent Technologies) respectively.
Hybridization protocol 600 ng of the obtained Cy3-labeled cRNA was 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 Human Sure Print GE 8x60 K v2 Microarrays (Agilent Technologies) (G4112A) 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.
Scan protocol Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner System (Scan Control Software 8.5, Agilent) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%)
Description gene expression after 24 hours
SCC13 skin tumor cell line stably transfected
Data processing Normalized Signal Intensity
Submission date Nov 15, 2016
Last update date Apr 23, 2018
Contact name Guergana Iotzova-Weiss
Organization name Dermatology Clinic Zurich
Street address Gloriastrasse 31
City Zurich
ZIP/Postal code 8091
Country Switzerland
Platform ID GPL16699
Series (1)
GSE89856 Differential gene expression profile of SCC13 tumor cells after TLR4 overexpression and LPS treatment
Reanalyzed by GSE113533

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

Data table
1 9.977869e+004
2 3.165075e+000
3 3.192626e+000
4 3.070611e+003
5 4.218585e+000
6 3.267639e+000
7 1.006326e+001
8 2.668188e+001
9 1.616880e+003
10 2.806073e+002
11 8.706340e+000
12 3.043596e+003
13 1.190445e+002
14 6.360648e+000
15 3.418701e+000
16 3.429046e+000
17 5.105784e+002
18 2.278108e+002
19 7.744630e+002
20 1.651806e+003

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.

Supplementary file Size Download File type/resource
GSM2391665_p1383_16_control_LPS.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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