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Sample GSM1562180 Query DataSets for GSM1562180
Status Public on Jan 31, 2019
Title 4_2mg_Cl_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: CI treated with nanomaterial (Carbo Iron 10 mg/l)
batch: four
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 11.9966279540518
2 4.16867211813223
3 4.30833903013941
4 4.36741475124683
5 5.21401549141084
6 8.5204345263119
7 9.18930337145282
8 4.46454575033394
9 11.3122093702477
10 4.81297947125148
11 7.10115497860052
12 6.41494944147426
13 9.33252613097627
14 4.55650605467193
15 14.1188257729268
16 5.19844504145236
17 11.8600412276721
18 6.94233122451058
19 8.40327837547105
20 9.71789058398728

Total number of rows: 62976

Table truncated, full table size 1398 Kbytes.

Supplementary file Size Download File type/resource
GSM1562180_US90203617_253124110010_S01_GE1_107_Sep09_1_3.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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