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Sample GSM1365149 Query DataSets for GSM1365149
Status Public on Apr 30, 2014
Title SBC-3 SALL4
Sample type RNA
Source name lung cancer cells_SALL4 vector
Organism Homo sapiens
Characteristics cell line: SBC-3
cell type: lung small cell calcinoma
transduced with: SALL4 vector (pCMV6-SALL4)
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 SALL4
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
4 387.4644267
5 3760.102929
6 124.1810517
7 20950.62695
8 2789.35489
9 15994.52747
10 62.61896671
11 18.81696319
12 2907.252137
13 5124.124604
14 1635.44906
15 31185.29851
16 72.57157438
17 308.9889788
18 89.25848101
19 39.31789292
20 2982.03595
21 3281.461668
24 364.8266314
25 2010.425965

Total number of rows: 58717

Table truncated, full table size 1015 Kbytes.

Supplementary file Size Download File type/resource
GSM1365149_AR1378_06raw.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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