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Sample GSM1486022 Query DataSets for GSM1486022
Status Public on Dec 31, 2023
Title neomycin_rep1
Sample type RNA
 
Source name neomycin_rep1
Organism Danio rerio
Characteristics tissue: whole body
age: 5 dpf
treatment: 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.
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 exposed to 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 6.804
A_15_P100009 6.642
A_15_P100011 7.463
A_15_P100012 8.617
A_15_P100015 8.992
A_15_P100023 10.802
A_15_P100025 12.089
A_15_P100026 6.121
A_15_P100027 6.403
A_15_P100028 5.658
A_15_P100038 7.223
A_15_P100046 8.199
A_15_P100049 8.07
A_15_P100050 9.714
A_15_P100052 11.049
A_15_P100054 12.642
A_15_P100059 10.118
A_15_P100063 7.521
A_15_P100069 7.939
A_15_P100071 7.273

Total number of rows: 25265

Table truncated, full table size 469 Kbytes.




Supplementary file Size Download File type/resource
GSM1486022_neo_n1.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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