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Sample GSM1967623 Query DataSets for GSM1967623
Status Public on Dec 09, 2015
Title CCCP Replicate 2
Sample type RNA
Source name C3A cells exposed 2h
Organism Homo sapiens
Characteristics cell line: C3A
Treatment protocol C3A cells were exposed for 2 hours to substances. For microarray analysis, 6 replicate wells per concentration were pooled. DMSO (0.1%) was used as solvent control.
Growth protocol C3A cells were grown in 75 cm2 culture flasks until approx. 80% confluency. Cells were then subcultured as quoted above until the uptake of trypsinised cells in media. C3A cells were diluted to reach a final density of 250 000 cells/ml. 200 µl of cell suspension were seeded in the inner 60 wells of a black 96-well plate with clear bottom (Greiner bio-one, Product 655906, Reinach, Switzerland). The outer rows were filled with 200 µl 1x PBS (phosphate buffered saline, Sigma-Aldrich, Buchs, Switzerland). Cells were pre-incubated at 37°C for 24 h. After pre-incubation cells were dosed with the test chemicals.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNeasy Mini Kit (QUIAGEN, Product 74104, Hombrechtikon, Switzerland) according to manufacturers’ instructions. DNA was digested using the RNeasy Mini Kit optional on-column DNase digestion. Quality of extracted RNA was checked via the Nanodrop 1000 spectraphotomoeter V3.7, as well as running the samples on a 1.5% agarose gel.
Label cy3
Label protocol For Microarray analysis, Agilent SurePrint G3 Human Gene Expression Microarrays (8x60K) were used in combination with a one-color based hybridization protocol (OneColor RNA Spike-In Mix, Agilent Technologies, number 51885282). All steps were carried out according to the manufacturer´s instructions.
Hybridization protocol After hybridization, the microarrays were washed using Gene Expression Wash Buffer Kit (Agilent Technologies),
Scan protocol Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction Software (Agilent Technologies).
Data processing The data was normalized using quantile-normalization. Control spots as well as not uniform spots were removed. The solvent control was averaged and the M value (log2FoldChange) calculated. Duplicated spots on the array were averaged before exposure replicates were averaged using the median.
Submission date Dec 08, 2015
Last update date Dec 09, 2015
Contact name Jessica Legradi
Organization name VU Amsterdam
Department IVM
Street address De Boelelaan 1087
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
Platform ID GPL13607
Series (2)
GSE75783 C3A Cells: Exposure vs Control [one-channel arrays]
GSE75784 Mode of toxic action assignment of chemicals

Data table header descriptions
VALUE normalized log2 signal values

Data table
1 0
2 0
3 0
4 6.753917364
5 8.324984046
6 5.32407341
7 10.89388964
8 8.380469074
9 4.701792443
10 5.636054099
11 4.870495173
12 9.451642413
13 9.471836848
14 7.429100803
15 12.23685552
16 5.365302524
17 7.332563388
18 4.718577809
19 4.654386274
20 9.964004633

Total number of rows: 62976

Table truncated, full table size 1048 Kbytes.

Supplementary file Size Download File type/resource
GSM1967623_RS-237_01_CCCP2.txt.gz 12.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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