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Sample GSM3003563 Query DataSets for GSM3003563
Status Public on May 01, 2018
Title larvae irradiated with 15Gy_IR2, biological rep3
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
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
VALUE RMA signal intensity

Data table
AFFX-BioB-3_at 263.1996858
AFFX-BioB-5_at 283.107255
AFFX-BioB-M_at 372.2286271
AFFX-BioC-3_at 708.5280226
AFFX-BioC-5_at 544.4413166
AFFX-BioDn-3_at 3070.48579
AFFX-BioDn-5_at 1285.380652
AFFX-CreX-3_at 9896.043162
AFFX-CreX-5_at 6457.317338
AFFX-DapX-3_at 348.139626
AFFX-DapX-5_at 53.61799404
AFFX-DapX-M_at 199.7220849
AFFX-Dr-AB076373-1_at 23.027974
AFFX-Dr-acta1-3_at 22491.32668
AFFX-Dr-acta1-5_at 2428.754371
AFFX-Dr-acta1-5_x_at 5173.798545
AFFX-Dr-acta1-M_at 11903.63676
AFFX-Dr-AF292559-1_at 10.32626207
AFFX-Dr-AF292559-2_s_at 4.656573401
AFFX-Dr-AF292559-3_s_at 4.499989893

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.

Supplementary file Size Download File type/resource
GSM3003563_140212-131145A_J3_Zebrafish_.CEL.gz 1.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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