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Sample GSM2454666 Query DataSets for GSM2454666
Status Public on Jan 13, 2017
Title BEECH_aerosol_rep1
Sample type RNA
Source name A549, beech aerosol
Organism Homo sapiens
Characteristics organ: lung
cell line: A549
tissue: epithelium
Treatment protocol Confluent layers of A549 cells were exposed to the diluted log wood and pellet combustion aerosols for 4 h. At the same time clean air exposures of confluent layers of A549 cells were performed as reference under the same conditions.
Growth protocol Human lung epithelial cell line A549 (ATCC® CCL-185™) was cultured in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS), 100 U/ml penicillin, 100 mg/ml streptomycin (all from Life Technologies, Darmstadt).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Rneasy Mini plus Kit (Qiagen) including genomic DNA removal according to the manufacturer s protocol.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol Purified labeled cRNA was fragmented and hybridized on Human Gene Expression Microarrays (Sure Print G3 Human Gene Expression Microarray 8x60 K, Agilent, Waldbronn, Germany) using ozone-barrier slide covers and hybridization gasket slides (Ozone-Barrier Slide Cover Kit, Hybridization Gasket Slide Kit and Gene Expression Hybridisation Kit, Agilent, Waldbronn, Germany) for 17h at 65°C in a hybridization oven.
Scan protocol After washing (Gene Expression Wash Buffer Kit, Agilent, Waldbronn, Germany) slides were scanned (Agilent C microarray scanner, Agilent, Waldbronn, Germany).
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 028004_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Jan 12, 2017
Last update date Jan 13, 2017
Contact name Sebastian Oeder
Organization name Technische Universität München
Department Center for Allergy and Environment (ZAUM)
Street address Biedersteinerstr. 29
City Munich
ZIP/Postal code 80802
Country Germany
Platform ID GPL13607
Series (1)
GSE93557 Lung cell responses to wood combustion aerosols

Data table header descriptions
VALUE Normalized signal intensity

Data table
1 1.41E+05
2 3.83E+00
3 3.80E+00
4 6.81E+02
5 1.64E+03
6 7.27E+01
7 5.13E+03
8 2.70E+03
9 3.66E+00
10 6.04E+01
11 4.26E+00
12 1.04E+03
13 8.93E+02
14 1.43E+03
15 2.77E+04
16 3.52E+00
17 1.03E+02
18 3.49E+00
19 3.47E+00
20 1.07E+03

Total number of rows: 62976

Table truncated, full table size 911 Kbytes.

Supplementary file Size Download File type/resource
GSM2454666_US11073879_252800421712_S01_GE1_1100_Jul11_1_1.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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