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Sample GSM1562188 Query DataSets for GSM1562188
Status Public on Jan 31, 2019
Title 5_2mg_24h
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: 24h
concentration: 2mg
nano: nCI (not treated with nanomaterial)
batch: five
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 11.6248097319834
2 4.36522884925154
3 4.27961058105249
4 4.47269083924278
5 5.25148241062021
6 9.98402898182538
7 8.02725808932367
8 4.39981195932568
9 11.9435507494383
10 4.73640193131829
11 7.72914273978008
12 7.03917610071501
13 7.96542356581013
14 4.79197682089869
15 14.63249295158
16 5.34706765716587
17 11.9005454999766
18 6.21992476886281
19 8.1130095649463
20 9.15008441798578

Total number of rows: 62976

Table truncated, full table size 1398 Kbytes.




Supplementary file Size Download File type/resource
GSM1562188_US90203617_253124110009_S01_GE1_107_Sep09_1_3.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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