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Sample GSM3319268 Query DataSets for GSM3319268
Status Public on Aug 06, 2021
Title sicontrol-3
Sample type RNA
Source name sicontrol
Organism Homo sapiens
Characteristics transfection: sicontrol
cell type: human lung squamous cell carcinoma
cell line: MCC148c
Treatment protocol The siRNA (siCD271 or si control) transfections were performed using Lipofectamine® RNAiMAX Reagent (Life Technologies, CA, USA) in antibiotic-free medium for 48 h.
Extracted molecule total RNA
Extraction protocol RNA from MCC148c cells was purified using RNeasy Mini Kits and QIAshredder columns (Qiagen, Canada).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng 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). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction buffer 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 SurePrint G3 Human Gene Expression 8x60K(G4851A) 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 Nitrogen gas.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression after 48hr lipofeation of sicontrol or siCD271 in lung sqmaous cell carcinoma cell line.
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Aug 06, 2018
Last update date Aug 06, 2021
Contact name Keiichi Tamai
Organization name Miyagi Cancer Center
Street address 1-47, Nodayama, Shiote, Medeshima
City Natori, Miyagi
ZIP/Postal code 981-1293
Country Japan
Platform ID GPL13607
Series (1)
GSE118141 CD271 is preferentially expressed and essential for cell proliferation in squamous cell carcinoma of the lung

Data table header descriptions
VALUE Normalized signal intensity

Data table
4 6.929780348
5 6.711223688
6 4.623610552
7 11.38980555
8 6.38806724
9 1.704489555
10 1.702387595
11 1.700474342
12 10.21624992
13 10.35295048
14 3.364551422
15 12.73479576
16 1.689463328
17 4.212209009
18 1.684294964
19 1.681606233
20 5.52419284
21 9.475668995
22 1.67465589
23 1.671800152

Total number of rows: 62969

Table truncated, full table size 1089 Kbytes.

Supplementary file Size Download File type/resource
GSM3319268_US80703200_252800421732_S01_GE1_107_Sep09_1_3sicont-3.txt.gz 11.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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