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Sample GSM1031929 Query DataSets for GSM1031929
Status Public on Dec 15, 2012
Title SAE_TiO2_10_24hr-1
Sample type RNA
Source name SAE cells exposed to 10 ug/ml TiO2-NB for 24hr, biological rep1
Organism Homo sapiens
Characteristics cell line: SAE
cell type: small airway epithelial
treatment: TiO2-NB
dose: 10 ug/ml
time: 24 hr
Treatment protocol For transcriptomics analysis, cells were suspended at 1 x 106 cells per ml and plated in 25 cm2 flasks at 5 x 106 cells/flask. The multi-walled carbon nanotubes (MWCNT) or titanium nanobelts (TiO2-NB) were added directly to the wells at specified concentrations (0, 10 or 100 µg/ml) in media. The cells were cultured for either 1 or 24 h. At the end of the culture period the adherent cells were washed once in PBS and the RNA was isolated as described below.
Growth protocol Small airway epithelial (SAE) cells were obtained from Lonza Walkersville Inc. Cells were maintained in Lonza Clonetics SABM media (cat # cc-3119) supplemented with Lonza Clonetics SAGM single quots (cat# cc-4124). For experimental conditions, adherent SAEC cells were washed with HBSS (cat# cc-5022) and trypsin (cat# cc-5012) was then used to dislodge the cells. A trypsin neutralizing solution (cat# cc-5002) was then added and the cells were centrifuged at 250 x g for 5 min. The supernatant was discarded and the cells were resuspended and counted as stated above. All cultures were maintained in 37°C water-jacketed CO2 incubators (ThermoForma).
Extracted molecule total RNA
Extraction protocol Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).
Label biotin
Label protocol Complementary DNA was synthesized from 3 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).
Hybridization protocol Biotin-labeled cRNA (15 µg) was fragmented to a size range between 50-200 bases for array hybridization. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
Scan protocol The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
Description Gene expression data from SAE cells exposed to 10 ug/ml TiO2-NB for 24hr
Data processing Raw intensity data were quantile normalized by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.
Submission date Nov 06, 2012
Last update date Dec 15, 2012
Contact name Susan C. Tilton
Organization name Oregon State University
Department AG Envr & Molec Toxicology
Street address 1007 ALS Bldg
City Corvallis
State/province OR
ZIP/Postal code 97331
Country USA
Platform ID GPL571
Series (2)
GSE42067 Three human cell types respond to multi-walled carbon nanotubes and titanium dioxide nanobelts with cell-specific transcriptomic and proteomic expression [SAE cells]
GSE42069 Three human cell types respond to multi-walled carbon nanotubes and titanium dioxide nanobelts with cell-specific transcriptomic and proteomic expression

Data table header descriptions
VALUE RMA-normalized log2 signal intensity

Data table
AFFX-BioB-5_at 8.353425
AFFX-BioB-M_at 8.559966
AFFX-BioB-3_at 8.449499
AFFX-BioC-5_at 9.596588
AFFX-BioC-3_at 9.878386
AFFX-BioDn-5_at 11.018916
AFFX-BioDn-3_at 12.207622
AFFX-CreX-5_at 13.178378
AFFX-CreX-3_at 13.448479
AFFX-DapX-5_at 7.0115285
AFFX-DapX-M_at 8.2533865
AFFX-DapX-3_at 8.850843
AFFX-LysX-5_at 4.4820657
AFFX-LysX-M_at 4.614685
AFFX-LysX-3_at 5.528411
AFFX-PheX-5_at 5.3040133
AFFX-PheX-M_at 5.930439
AFFX-PheX-3_at 6.8168163
AFFX-ThrX-5_at 5.99412
AFFX-ThrX-M_at 5.7637253

Total number of rows: 22277

Table truncated, full table size 443 Kbytes.

Supplementary file Size Download File type/resource
GSM1031929_GO25.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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