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Sample GSM1502033 Query DataSets for GSM1502033
Status Public on Sep 11, 2014
Title Control for CNT-1 or CNT-2_NR8383
Sample type RNA
Source name Rat alveolar macrophages, 24hr, solvent control (BSA) for CNT-1 or CNT-2, replicate 4
Organism Rattus norvegicus
Characteristics cell type: alveolar macrophages
cell line: NR8383
treatment: untreated control for CNT-1 or CNT-2
time: 24h
Treatment protocol The culture medium were replaced by two kinds of the working solutions including impurity-free single-wall carbon nanotubes (CNT-1 or CNT-2), respectively. These working solutions were dissolved in 1mg/mL bovine serum albumin (BSA). Cell concentrations at this point were approximately 2.0 x 10^5 cells/mL. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.
Growth protocol Rat alveolar macrophages NR8383 were seeded into each well of a 96-well plate and grown in the F-12K with 15% heat-inactivated fetal bovine serum medium for 24 hours.
Extracted molecule total RNA
Extraction protocol After 24 hours, total RNA was extracted from the cells using the RNeasy mini (Qiagen, Tokyo, Japan) according to the manufactures instructions. Total 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 Rat Genome Oligo Microarrays (G4131F) 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 rat alveolar macrophages as cotrol for CNT-1
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09). 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.
Submission date Sep 10, 2014
Last update date Sep 11, 2014
Contact name Katsuhide Fujita
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 GPL7294
Series (1)
GSE61319 Gene expression profiles in rat alveolar macrophages exposure to impurity-free single-wall carbon nanotubes

Data table header descriptions
VALUE log2 average normalized signal intensity

Data table
A_44_P465448 0.148
A_44_P514796 0.061
A_44_P409518 0.026
A_44_P279262 0.036
A_44_P375042 0.011
A_44_P269499 0.016
A_44_P204808 0.157
A_44_P438090 0.001
A_44_P330643 0.006
A_44_P421941 0.161
A_42_P504653 0.039
A_44_P260580 -0.050
A_44_P445440 0.165
A_44_P313825 -0.021
A_44_P788423 0.038
A_44_P549509 -0.004
A_43_P12354 -0.004
A_43_P14989 -0.003
A_44_P172767 0.161
A_44_P884555 0.012

Total number of rows: 41103

Table truncated, full table size 774 Kbytes.

Supplementary file Size Download File type/resource
GSM1502033_CN400_001_control.normalized.tar.gz 1.5 Mb (ftp)(http) TAR
GSM1502033_CN400_001_control.raw.tar.gz 36.0 Mb (ftp)(http) TAR
Processed data included within Sample table
Processed data provided as supplementary file

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