NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1008539 Query DataSets for GSM1008539
Status Public on Sep 25, 2012
Title A549_24hr_CNT-3
Sample type RNA
 
Source name Alveolar epithelial cell, 24hr, CNT-3, replicate 4
Organism Homo sapiens
Characteristics cell type: Alveolar epithelial cell
cell line: A549
treatment: CNT-3
time: 24h
Treatment protocol Each medium were replaced by three kinds of single-wall carbon nanotubes (SWCNTs), CNT-1, CNT-2 or CNT-3 in a 10-fold dilution series. Cell concentrations at this point were approximately 1.3 x 10^5 cells/mL. The cultures were incubated for 24 or 48 hours at 37 ºC in a humidified incubator with 5% CO2.
Growth protocol Human alveolar epithelial cell line A549 were seeded into each well of a 96-well plate (Becton, Dickinson and Company, Franklin Lakes, NJ) and grown in the DMEM with 10% heat-inactivated fetal bovine serum medium for 24 hours.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the cells using the QIAcube instrument (Qiagen, Tokyo, Japan) following the manufactures instructions. RNA was quantified using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA) 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 RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Tokyo, Japan). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
 
Hybridization protocol Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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 (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um).
Description Gene expression after 24hr in CNT-3-exposed human alveolar epithelial cell
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v1_Sep09 and Grid: 026652_D_F_20110819). Background detrend: On (Feat NCRange, LoPass). Multiplicative detrend: True. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized data is the average of n=4. VALUE: Normalized signal intensity (log2)
 
Submission date Sep 24, 2012
Last update date Sep 25, 2012
Contact name Katsuhide Fujita
E-mail(s) ka-fujita@aist.go.jp
Organization name National Institute of Advanced Industrial Science and Technology
Department Research Institute of Science for Safety and Sustainability
Street address Onogawa 16-1
City Tsukuba
ZIP/Postal code 3058569
Country Japan
 
Platform ID GPL13497
Series (1)
GSE41101 Gene expression profiles in human alveolar epithelial cell line exposure to impurity-free single-wall carbon nanotubes

Data table header descriptions
ID_REF
VALUE log2 average normalized signal intensity

Data table
ID_REF VALUE
A_23_P146146 1.2389
A_23_P42935 -0.4401
A_23_P117082 0.5446
A_23_P2683 -0.3740
A_24_P358131 1.3162
A_33_P3367647 1.2399
A_23_P157316 -0.1144
A_32_P14850 -0.6731
A_23_P158596 0.7969
A_23_P350107 -0.8067
A_23_P388190 -0.7125
A_23_P106544 0.3347
A_33_P3219745 1.2226
A_32_P85539 -0.6444
A_23_P94998 -0.1953
A_33_P3235677 1.2096
A_23_P417014 1.2048
A_23_P103905 0.1556
A_24_P497186 -1.1158
A_23_P118536 1.0799

Total number of rows: 34181

Table truncated, full table size 686 Kbytes.




Supplementary file Size Download File type/resource
GSM1008539_CN100_006_1.txt.gz 9.1 Mb (ftp)(http) TXT
GSM1008539_CN100_006_2.txt.gz 9.1 Mb (ftp)(http) TXT
GSM1008539_CN100_006_3.txt.gz 9.2 Mb (ftp)(http) TXT
GSM1008539_CN100_006_4.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap