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Sample GSM1562170 Query DataSets for GSM1562170
Status Public on Jan 31, 2019
Title 3_K1_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: Control
time point: 12h
concentration: 0mg
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 12.5477154461633
2 4.04848687399234
3 5.71596199025514
4 5.05934446082443
5 4.91960823860325
6 8.69245204511179
7 8.52310246488896
8 4.20701432017753
9 11.45469288333
10 4.66177809777199
11 7.85914649542596
12 7.09803208296053
13 9.5908793952606
14 4.24555270625568
15 14.4367237401971
16 5.2240016741981
17 12.2572128728957
18 6.88149638481011
19 8.47437139675156
20 9.86683217270594

Total number of rows: 62976

Table truncated, full table size 1397 Kbytes.




Supplementary file Size Download File type/resource
GSM1562170_US90203617_253124110007_S01_GE1_107_Sep09_1_1.txt.gz 12.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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