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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.
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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.
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|
|
|
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)
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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 |
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