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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
E-mail(s) ytabu@cts.u-toyama.ac.jp
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
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
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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