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Status |
Public on Dec 31, 2023 |
Title |
tacrine_neomycin_rep3 |
Sample type |
RNA |
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Source name |
tacrine_neomycin_rep3
|
Organism |
Danio rerio |
Characteristics |
tissue: whole body age: 5 dpf treatment: tacrine and neomycin
|
Treatment protocol |
Zebrafish was pretreated with tacrine (50 uM) or DMSO (1%) for 1 hour and treated with neomycin (200 uM) or the vehicle for 1 hour.
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Growth protocol |
Zebrafish was maintained in fish medium (0.07 mM KCl, 2 mM CaCl2, 0.5 mM MgSO4, 0.7 mM NaHCO3, pH 7.4).
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from zebrafish whole body using RNAqueous-Micro Kit (Life Technologies, Carlsbad, CA), qualified by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), and quantified using using Nano Drop ND-100 (Wilmington, DE, USA).
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Label |
Cy3
|
Label protocol |
Cy3 labeled cRNA was prepared from 0.2 ug RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
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Hybridization protocol |
1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 uL containing fragmentation buffer and blocking agent according to the manufacture's protocol. After the fragmentation, 55 uL of hybridization buffer was added to the fragmentation mixture. For each reaction 100 uL was hybridized to an Agilent Zebrafish DNA Oligo Microarray (GPL14688) for 17 hours at 65°C in a rotating hybridization chamber. After the hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1, 1 minute with 37°C GE Wash buffer 2.
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Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.
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Description |
Gene expression in zebrafish exposed to tacrine and neomycin
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Data processing |
The scanned images were analyzed with Feature Extraction Software 8.0 (Agilent). The data was normalized using Agi4x44PreProcess in Bioconductor. Features flagged in gIsSaturated, gIsFeatNonUnifOL, gIsPosAndSignif and gIsWellAboveBG were excluded from further analysis.
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Submission date |
Aug 25, 2014 |
Last update date |
Dec 31, 2023 |
Contact name |
Yuhei Nishimura |
E-mail(s) |
yuhei@med.mie-u.ac.jp
|
Phone |
81-59-231-5411
|
Organization name |
Mie University Graduate School of Medicine
|
Department |
Integrative Pharmacology
|
Street address |
2-174 Edobashi
|
City |
Tsu |
State/province |
Mie |
ZIP/Postal code |
514-8507 |
Country |
Japan |
|
|
Platform ID |
GPL14664 |
Series (1) |
GSE60696 |
Transcriptome analysis of zebrafish exposed to neomycin and/or tacrine |
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