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Sample GSM1365148 Query DataSets for GSM1365148
Status Public on Apr 30, 2014
Title SBC-3 control
Sample type RNA
Source name lung cancer cells_control vector
Organism Homo sapiens
Characteristics cell line: SBC-3
cell type: lung small cell calcinoma
transduced with: control vector (pCMV6-Mock)
time point: 24h after transduction
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Mini Kit (QIAGEN), according to the protocol provided by the manufacturer.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).
Hybridization protocol 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60Karray slides (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 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
Description SBC-3 control
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028004_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Apr 08, 2014
Last update date Apr 30, 2014
Contact name Nozomi Yanagihara
Organization name Sapporo Medical University School of Medicine
Department Department of Clinical Laboratory Medicine
Street address South-1, West-16, Chuo-Ku
City Sapporo
ZIP/Postal code 060-8543
Country Japan
Platform ID GPL13607
Series (1)
GSE56595 Significance of SALL4 as a drug resistant factor in lung cancer

Data table header descriptions
VALUE Normalized signal intensity

Data table
4 368.810825
5 3429.728651
6 85.45206807
7 21481.44177
8 1362.630656
9 18115.25715
10 67.778649
11 11.20150461
12 3041.810503
13 5939.729447
14 1246.299556
15 34029.17657
16 11.29698695
17 211.1667506
18 71.43428427
19 11.31150279
20 2817.801221
21 3328.277151
24 294.2297912
25 1773.084729

Total number of rows: 58717

Table truncated, full table size 1015 Kbytes.

Supplementary file Size Download File type/resource
GSM1365148_AR1378_05raw.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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