| Sample GSM1031925 | Query DataSets for GSM1031925 |
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| Status | Public on Dec 15, 2012 |
| Title | SAE_MWCNT_10_24hr-3 |
| Sample type | RNA |
| Source name | SAE cells exposed to 10 ug/ml MWCNT for 24hr, biological rep3 |
| Organism | Homo sapiens |
| Characteristics | cell line: SAEcell type: small airway epithelialtreatment: MWCNTdose: 10 ug/mltime: 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 MWCNT 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 |
| E-mail(s) | Susan.Tilton@oregonstate.edu |
| 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 |
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