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Sample GSM3003562 Query DataSets for GSM3003562
Status Public on May 01, 2018
Title larvae irradiated with 15Gy_IR2, biological rep2
Sample type RNA
 
Source name zebrafish larva_15 Gy radiation
Organism Danio rerio
Characteristics strain: AB
development stage: 7 days post fertalization
tissue: lavae
irradiated with: 15 Gy radiation
Treatment protocol Embryos were attained from multiple clutches for each experimental procedure.The proton beam energy was 8 MeV/u, and the dose rate was 7.5 Gy/min.20 embryos were collected as one sample and stored at −80 ◦C to perform subsequent experiment of RNA extraction and mRNA transcription analysis.
Growth protocol The embryos were collected and rinsed with standard zebrafish E3 culture medium (5 mM NaCl, 0.33 mM CaCl2, 0.33 mM MgSO4, 0.15 mM KCl, pH 7.2, conductivity range 470–520 μS), and then, incubated at 28.5 ◦C incubator until experimental use.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GeneChip® Scanner 3000.
Description Gene expression data from zebrafish larvae 7 dpf
zebrafish_15Gy-02
Data processing The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Feb 13, 2018
Last update date May 01, 2018
Contact name Baoquan Zhao
Organization name Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences
Street address Taiping road,27
City Beijing
ZIP/Postal code 100850
Country China
 
Platform ID GPL1319
Series (1)
GSE110583 Toxic effects and foundation of proton radiation on the early-life stage of zebrafish development

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 278.340233
AFFX-BioB-5_at 345.0857503
AFFX-BioB-M_at 431.3359557
AFFX-BioC-3_at 761.0261196
AFFX-BioC-5_at 601.7656057
AFFX-BioDn-3_at 3519.036693
AFFX-BioDn-5_at 1297.22098
AFFX-CreX-3_at 10346.32224
AFFX-CreX-5_at 6586.156579
AFFX-DapX-3_at 493.3946532
AFFX-DapX-5_at 70.81467528
AFFX-DapX-M_at 285.2850529
AFFX-Dr-AB076373-1_at 25.4263975
AFFX-Dr-acta1-3_at 17503.75828
AFFX-Dr-acta1-5_at 612.097624
AFFX-Dr-acta1-5_x_at 1392.323593
AFFX-Dr-acta1-M_at 6071.888183
AFFX-Dr-AF292559-1_at 10.96613371
AFFX-Dr-AF292559-2_s_at 4.698957044
AFFX-Dr-AF292559-3_s_at 5.365147301

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM3003562_140212-131145A_J2_Zebrafish_.CEL.gz 1.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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