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Sample GSM1562171 Query DataSets for GSM1562171
Status Public on Jan 31, 2019
Title 3_1mg_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: 1mg
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
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
1 13.8255380210611
2 4.25620868852739
3 4.09934781040319
4 4.09934781040319
5 4.7515440590891
6 9.8600442597193
7 8.21890373984013
8 4.20579324939716
9 11.8647242009035
10 4.36413465500805
11 7.88178313640099
12 7.6052480015658
13 9.3251121738577
14 4.31061278165953
15 14.4640132083761
16 6.34318571544788
17 12.1039639132627
18 7.15228484230658
19 7.83930222190047
20 9.960115090833

Total number of rows: 62976

Table truncated, full table size 1396 Kbytes.

Supplementary file Size Download File type/resource
GSM1562171_US90203617_253124110007_S01_GE1_107_Sep09_1_2.txt.gz 12.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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