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Sample GSM1486019 Query DataSets for GSM1486019
Status Public on Dec 31, 2023
Title control_rep1
Sample type RNA
 
Source name control_rep1
Organism Danio rerio
Characteristics tissue: whole body
age: 5 dpf
treatment: none
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.
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).
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).
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.
 
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.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.
Description Gene expression in zebrafish without treatment of tacrine and neomycin
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.
 
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

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_15_P100008 6.651
A_15_P100009 6.592
A_15_P100011 7.45
A_15_P100012 8.771
A_15_P100015 9.184
A_15_P100023 11.095
A_15_P100025 12.156
A_15_P100026 6.124
A_15_P100027 6.326
A_15_P100028 5.658
A_15_P100038 7.339
A_15_P100046 8.257
A_15_P100049 7.901
A_15_P100050 9.264
A_15_P100052 11.127
A_15_P100054 12.564
A_15_P100059 10.671
A_15_P100063 7.381
A_15_P100069 7.8
A_15_P100071 7.653

Total number of rows: 25265

Table truncated, full table size 469 Kbytes.




Supplementary file Size Download File type/resource
GSM1486019_cont_n1.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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