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Sample GSM5614075 Query DataSets for GSM5614075
Status Public on Mar 05, 2022
Title BEAS_4mg_6h50min_Pollen_rep2
Sample type RNA
 
Source name BEAS-2B cells
Organism Homo sapiens
Characteristics time: 6h50min
condition: pollen
Treatment protocol BEAS-2B cells were cultured in 6-well Transwells with BEGM Medium. After 24h, basal medium was changed, apical medium was removed and cells were kept in air-liquid interface for 24h, before exposure. For combined expousre, cells were exposed to diesel CAST model aerosol for 2hours (or clean air), in an vitro exposure system. After that, basal medium was changed and cells were placed in a cell culture incubator for 24 hours. After that, all cells were exposed to 4 mg of whole birch pollen dispersing it with 0.5 bar pressured air into the Pollen Sedimentation Chamber, for different incubation times. Cells were kept all the time at 37°C and 5% CO2. For the pollen exposure alone, the same amount of birch pollen was used (4mg) and exposure was performed as explained above.
Extracted molecule total RNA
Extraction protocol RNA was obtained with the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany), with additional 1% ß-Mercaptoethanol (Roth, Karlsruhe, Germany), according to the manufacturer’s protocol. The quantification and quality of the RNA was assessed with an UV-vis spectrophotometer (NanoPhotometer® N60, IMPLEN, Munich, Germany) and the Agilent 2100 Bioanalyzer RNA Nano chip (Agilent Technologies, Waldbronn, Germany), respectively.
Label Cy3
Label protocol RNA samples (input of 100ng) were spiked (One-Color RNA Spike-in Kit, Agilent Technologies, Waldbronn, Germany), Cy3-labelled (Low Input Quick Amp Labeling Kit, one-color, Agilent Technologies, Waldbronn, Germany) and purified on RNeasy mini spin columns (QIAGEN). Generated Cy3-labelled cRNA was quantified with NanoPhotometer® N60, IMPLEN, Munich, Germany.
 
Hybridization protocol The Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes with Agilent fragmentation mix, according to the manufacturers instructions. After that, 25uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and 40uL of the samples was hybridized to One-Color SurePrint G3 8x60K Human gene expression arrays (Agilent Technologies, Inc, Waldbronn, Germany) for 17 hours at 65°C in a rotating Agilent hybridization oven. After incubation time, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1, at 500rpm and 1 minute with 32°C GE Wash buffer 2 (Agilent), at 500rpm. Slide was placed in a array gasket chamber for scan procedure.
Scan protocol Slides were scanned using the Agilent DNA Microarray Scanner using one color scan setting for 8x60k G3 array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).
Description Gene expression after 6h50min in 4 mg whole birch pollen exposure
Data processing Scanned images were analyzed with Feature Extraction Software Version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20200924) to obtain background and Processed Signal intensities.
 
Submission date Oct 05, 2021
Last update date Mar 05, 2022
Contact name Joana Candeias
Organization name Technical University Munich & Helmholtz Center Munich
Department Center Allergy and Environment (ZAUM)
Lab Prof. Dr. Jeroen Buters Lab
Street address Biedersteinerstr. 29
City Munich
ZIP/Postal code 80802
Country Germany
 
Platform ID GPL13607
Series (1)
GSE185399 Effect of the primed exposure of Diesel CAST model aerosol in air-liquid interface BEAS-2B cells exposed to native birch pollen

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
4 9.75
5 11.38
6 6.71
7 12.39
8 9.38
9 7.58
10 6.86
11 6.51
12 11.08
13 10.96
14 8.67
15 14.77
16 6.46
17 8.23
18 6.45
19 7.15
20 10.43
21 10.85
24 8.39
25 8.77

Total number of rows: 59025

Table truncated, full table size 638 Kbytes.




Supplementary file Size Download File type/resource
GSM5614075_B4mg6hP2.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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