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Sample GSM3016154 Query DataSets for GSM3016154
Status Public on Feb 12, 2019
Title muscle_WIK_PCB-exposed_male_vs_Casper_3
Sample type genomic
 
Channel 1
Source name white muscle from adult WIK male
Organism Danio rerio
Characteristics age: adult
tissue: white muscle
strain: WIK
treatment: 130 ng/L PCB-126
Sex: male
Extracted molecule genomic DNA
Extraction protocol Muscle tissue was collected from adult zebrafish housed within the Brown lab zebrafish facility for 2 generations. AB, Tuebingen, and WIK zebrafish were originally sourced from ZIRC (Eugene, OR) as batches of 100 embryos. Individuals were sexed via visual identification of eggs or testes at the time of dissection. Pooled Casper samples were collected from 30 homogenized whole fish. Total DNA was extracted on Qiagen DNeasy columns per the manufacturer's protocol. Nucleic acid concentrations were determined on a Nanodrop Spectrophotometer 2000.
Label Cy5
Label protocol Custom designed 1x1M zebrafish whole genome CGH arrays, BioPrime array CGH labeling kit (Invitrogen), and Cyanine-3/5 labeled dCTP (Perkin Elmer) were used following manufacturer’s protocols. AB, Tuebingen, and WIK were labeled with Cy-5 and Caseper was labeled with Cy-3. Labeled DNA was purified on Amicon Ultra (Millipore) columns with 0.1X SSC per the manufacturer’s protocol and quantified on a NanoDrop spectrophotometer.
 
Channel 2
Source name whole body homogenate from pooled Casper adults
Organism Danio rerio
Characteristics strain: Casper
age: adult
tissue: whole body homogenate
Extracted molecule genomic DNA
Extraction protocol Muscle tissue was collected from adult zebrafish housed within the Brown lab zebrafish facility for 2 generations. AB, Tuebingen, and WIK zebrafish were originally sourced from ZIRC (Eugene, OR) as batches of 100 embryos. Individuals were sexed via visual identification of eggs or testes at the time of dissection. Pooled Casper samples were collected from 30 homogenized whole fish. Total DNA was extracted on Qiagen DNeasy columns per the manufacturer's protocol. Nucleic acid concentrations were determined on a Nanodrop Spectrophotometer 2000.
Label Cy3
Label protocol Custom designed 1x1M zebrafish whole genome CGH arrays, BioPrime array CGH labeling kit (Invitrogen), and Cyanine-3/5 labeled dCTP (Perkin Elmer) were used following manufacturer’s protocols. AB, Tuebingen, and WIK were labeled with Cy-5 and Caseper was labeled with Cy-3. Labeled DNA was purified on Amicon Ultra (Millipore) columns with 0.1X SSC per the manufacturer’s protocol and quantified on a NanoDrop spectrophotometer.
 
 
Hybridization protocol Samples with specific activity between 20-60 (where [dye pmol/uL]/[DNA ng/uL]*1000 = specific activity) were fragmented, hybridized to array slides at 65°C for 40 hours, washed briefly, and scanned on an Agilent SureScan array scanner.
Scan protocol Data were extracted from raw TIFF files using Agilent FeatureExtraction software with grid file 049635_D_F_20130524 and scan protcol CGH_1100_Jul11.
Description WIK PCB-exposed male vs Casper, replicate 3
WIK_PCB_N
Data processing Normalized, background subtracted log10 ratios of processed Red signal/processed Green signal (strain/Casper) via Agilent FeatureExtraction software. Processed data files contain Log10 ratios of processed Red signal/processed Green signal (test/reference = strain/Casper)
 
Submission date Feb 16, 2018
Last update date Feb 12, 2019
Contact name Kim H Brown
E-mail(s) kibr2@pdx.edu
Organization name Portland State University
Department Department of Biology
Lab Brown Lab
Street address 1719 SW 10th Ave
City Portland
State/province OR
ZIP/Postal code 97201
Country USA
 
Platform ID GPL24619
Series (1)
GSE110763 Strain-specific CNV in zebrafish treated with PCB-126, vehicle control, or untreated

Supplementary file Size Download File type/resource
GSM3016154_WIK_PCB_N.txt.gz 99.3 Mb (ftp)(http) TXT
Processed data are available on Series record

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