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Sample GSM938377 Query DataSets for GSM938377
Status Public on Jul 01, 2012
Title PC9 GR3 DMSO
Sample type RNA
Source name PC9 GR3
Organism Homo sapiens
Characteristics cell line: PC-9
gefitinib-resistant: yes
treatment: DMSO
Treatment protocol For RNA collection, 8 × 10^4 cells were seeded per well in 6-well plates and allowed to attach for 24 hours. The cells were then treated with 1uM gefitinib, 48hrs later we collected total RNA from these cell line.
Growth protocol PC9 cell lines were cultured by RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the RNAeasy kit (QIAGEN, , Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 175 ng RNA using Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) 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 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 8x60K human array (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).
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting.
Description Gene expression after 48hrs in 0uM Gefitinib human lung cancer cell line
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1010_Sep10) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date May 29, 2012
Last update date Jul 01, 2012
Contact name Junko Hamamoto
Organization name School of Medicine, Keio University
Department Pulmonary Medicine
Street address 35 Shinanomachi, Shinjuku-ku
City Tokyo
ZIP/Postal code 160-8582
Country Japan
Platform ID GPL13607
Series (1)
GSE38302 Analysis of gene expression change by gefitinib treatment in gefitinib sensitive PC9 and resistant PC9.

Data table header descriptions
VALUE gProcessedSignal

Data table
1 1.22E+05
2 6.79E+00
3 6.83E+00
4 3.01E+02
5 1.45E+03
6 6.22E+01
7 8.33E+03
8 3.37E+03
9 7.01E+00
10 2.41E+02
11 7.05E+00
12 1.84E+03
13 2.83E+02
14 1.37E+03
15 1.67E+04
16 7.11E+00
17 2.85E+02
18 7.12E+00
19 7.12E+00
20 2.41E+03

Total number of rows: 62976

Table truncated, full table size 911 Kbytes.

Supplementary file Size Download File type/resource
GSM938377_US82600146_252800412598_S01_GE1_1010_Sep10_2_1.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data provided as supplementary file
Processed data are available on Series record
Processed data included within Sample table

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