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Sample GSM1562175 Query DataSets for GSM1562175
Status Public on Jan 31, 2019
Title 3_8mg_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: 8mg
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 12.8449784748766
2 4.3151495622563
3 4.51175265376738
4 4.4797802640291
5 5.16364967601583
6 9.36379254904717
7 8.81890666748684
8 4.66266837551754
9 11.7612265687558
10 4.57648434679685
11 7.56236168971454
12 7.22565933829125
13 9.70738609607533
14 4.54399845013454
15 14.5265250286082
16 5.76652890859886
17 12.3431206386048
18 7.35238832886454
19 8.66472504104965
20 9.88269080727902

Total number of rows: 62976

Table truncated, full table size 1393 Kbytes.

Supplementary file Size Download File type/resource
GSM1562175_US90203617_253124110007_S01_GE1_107_Sep09_2_2.txt.gz 12.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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