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Sample GSM1031913 Query DataSets for GSM1031913
Status Public on Dec 15, 2012
Title SAE_MWCNT_100_1hr-3
Sample type RNA
 
Source name SAE cells exposed to 100 ug/ml MWCNT for 1hr, biological rep3
Organism Homo sapiens
Characteristics cell line: SAE
cell type: small airway epithelial
treatment: MWCNT
dose: 100 ug/ml
time: 1 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 100 ug/ml MWCNT for 1hr
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

Data table header descriptions
ID_REF
VALUE RMA-normalized log2 signal intensity

Data table
ID_REF VALUE
AFFX-BioB-5_at 8.567863
AFFX-BioB-M_at 8.76664
AFFX-BioB-3_at 8.552421
AFFX-BioC-5_at 9.70855
AFFX-BioC-3_at 9.965883
AFFX-BioDn-5_at 11.039245
AFFX-BioDn-3_at 12.18238
AFFX-CreX-5_at 13.175493
AFFX-CreX-3_at 13.427332
AFFX-DapX-5_at 7.298886
AFFX-DapX-M_at 8.594161
AFFX-DapX-3_at 8.99842
AFFX-LysX-5_at 4.455357
AFFX-LysX-M_at 4.788327
AFFX-LysX-3_at 5.610904
AFFX-PheX-5_at 5.286664
AFFX-PheX-M_at 5.6077437
AFFX-PheX-3_at 6.8811145
AFFX-ThrX-5_at 5.759175
AFFX-ThrX-M_at 5.8703747

Total number of rows: 22277

Table truncated, full table size 443 Kbytes.




Supplementary file Size Download File type/resource
GSM1031913_GO09.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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