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Sample GSM3003560 Query DataSets for GSM3003560
Status Public on May 01, 2018
Title larvae irradiated with 12Gy_IR1, biological rep1
Sample type RNA
 
Source name zebrafish larva_12 Gy radiation
Organism Danio rerio
Characteristics strain: AB
development stage: 7 days post fertalization
tissue: lavae
irradiated with: 12 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_12Gy-01
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 431.6466676
AFFX-BioB-5_at 402.4305085
AFFX-BioB-M_at 621.5683356
AFFX-BioC-3_at 1034.955384
AFFX-BioC-5_at 865.3460317
AFFX-BioDn-3_at 4608.970895
AFFX-BioDn-5_at 1883.499234
AFFX-CreX-3_at 13236.69865
AFFX-CreX-5_at 7859.28316
AFFX-DapX-3_at 720.9937092
AFFX-DapX-5_at 99.40618386
AFFX-DapX-M_at 435.0972713
AFFX-Dr-AB076373-1_at 27.15663938
AFFX-Dr-acta1-3_at 21150.37743
AFFX-Dr-acta1-5_at 747.7500235
AFFX-Dr-acta1-5_x_at 2159.63953
AFFX-Dr-acta1-M_at 10115.32243
AFFX-Dr-AF292559-1_at 8.67923207
AFFX-Dr-AF292559-2_s_at 5.297222791
AFFX-Dr-AF292559-3_s_at 5.677555804

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM3003560_140212-131145A_J11_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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