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Sample GSM4904003 Query DataSets for GSM4904003
Status Public on Nov 12, 2020
Title 2_BcP: benzo[c]phenanthrene (BcP)-treated
Sample type RNA
Source name zebrafish scales
Organism Danio rerio
Characteristics tissue: scale
Treatment protocol The scales were incubated at 15 °C for 6 h in Leibovitz's L-15 medium (Invitrogen, Grand Island, NY, USA) with benzo[c]phenanthrene (BcP: 1 nM) or 3-hydroxybenzo[c]phenanthrene (3-OHBcP: 1 nM).
Growth protocol Scales were collected from zebrafish under anesthesia.
Extracted molecule total RNA
Extraction protocol Total RNAs were prepared from zebrafish scales using a total RNA isolation kit for fibrous tissue (Qiagen GmbH, Hilden, Germany) and treated with DNase I (RNase-Free DNase kit, Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >8.5 were considered acceptable.
Label biotin
Label protocol 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).
Hybridization protocol After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.
Scan protocol The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).
Description Scales were incubated with BcP at 15°C for 6 h.
Data processing GeneChip Analysis Suite (Expression Console)
Submission date Nov 11, 2020
Last update date Nov 12, 2020
Contact name Yoshiaki Tabuchi
Organization name University of Toyama
Department Life Science Research Center
Lab Division of Molecular Genetics Research
Street address 2630 Sugitani
City Toyama
State/province Toyama
ZIP/Postal code 930-0194
Country Japan
Platform ID GPL1319
Series (1)
GSE161253 Effects of polycyclic aromatic hydrocarbons on osteoclasts and osteoblasts in the scales of zebrafish

Data table header descriptions
VALUE log2 RMA signal

Data table
AFFX-BioB-5_at 7.74574
AFFX-BioB-M_at 7.96211
AFFX-BioB-3_at 7.16768
AFFX-BioC-5_at 8.53333
AFFX-BioC-3_at 8.88407
AFFX-BioDn-5_at 9.58132
AFFX-BioDn-3_at 10.9299
AFFX-CreX-5_at 11.6733
AFFX-CreX-3_at 12.4378
AFFX-DapX-5_at 5.79917
AFFX-DapX-M_at 8.18775
AFFX-DapX-3_at 9.24319
AFFX-LysX-5_at 4.62314
AFFX-LysX-M_at 5.99977
AFFX-LysX-3_at 6.40743
AFFX-PheX-5_at 5.09005
AFFX-PheX-M_at 6.19567
AFFX-PheX-3_at 7.54528
AFFX-ThrX-5_at 4.62706
AFFX-ThrX-M_at 5.05161

Total number of rows: 15617

Table truncated, full table size 375 Kbytes.

Supplementary file Size Download File type/resource
GSM4904003_2-BcP.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM4904003_2-BcP.chp.gz 140.1 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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