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Sample GSM1562172 Query DataSets for GSM1562172
Status Public on Jan 31, 2019
Title 3_2mg_12h
Sample type RNA
 
Source name mRNA from pooled whole zebrafish embryos, labeled with Cyanine-3 (green)
Organism Danio rerio
Characteristics tissue: whole embryo
treatment: PCE
time point: 12h
concentration: 2mg
nano: nCI (not treated with nanomaterial)
batch: three
Extracted molecule total RNA
Extraction protocol Trizol followed by RNeasy MiniKit cleanup (Qiagen) using the manufacturers’ protocols
Label Cy3
Label protocol One-Color Quick Amp Labeling Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany)
 
Hybridization protocol One-Color Quick Amp Labeling Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany)
Scan protocol Agilent DNA Microarray Scanner and Agilent Feature Extraction Software V11.5.1.1, according to manufacturer's protocol.
Data processing Background subtraction, Quantile normalization between arrays
Software for data normalization:
R software for windows (V2.15) package limma (V3.16.5)
 
Submission date Dec 09, 2014
Last update date Jan 31, 2019
Contact name Andreas SchĂĽttler
E-mail(s) schuettler@bafg.de
Organization name German Federal Institute of Hydrology
Department Department Biochemistry and Ecotoxicology
Street address Am Mainzer Tor 1
City Koblenz
ZIP/Postal code 56068
Country Germany
 
Platform ID GPL19526
Series (1)
GSE63994 Concentration dependent gene expression in zebrafish embryos after PCE exposure

Data table header descriptions
ID_REF Agilent feature number
VALUE log2-transformed, background corrected, quantile normalized intensity values

Data table
ID_REF VALUE
1 13.9745742355784
2 4.17117679765177
3 4.13057056280543
4 4.17117679765177
5 4.80654962198596
6 9.60150965925543
7 8.50971315907815
8 4.45327063401062
9 11.9110935022405
10 4.31741261376487
11 7.63832277474869
12 6.67109872574847
13 9.36703928496646
14 4.17117679765177
15 13.4428604989831
16 6.44656640906607
17 11.7853886080766
18 7.16176174330467
19 8.19606416592105
20 9.73714169365265

Total number of rows: 62976

Table truncated, full table size 1399 Kbytes.




Supplementary file Size Download File type/resource
GSM1562172_US90203617_253124110007_S01_GE1_107_Sep09_1_3.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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