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Sample GSM3032612 Query DataSets for GSM3032612
Status Public on Feb 27, 2019
Title zPer2 zCry1a zCry2a triple KO (TKO) zebrafish treated with 3-h light
Sample type RNA
 
Source name TKO 3-h light
Organism Danio rerio
Characteristics treatment: 3h light
genotype: zPer2 zCry1a zCry2a triple KO
tissue: Whole body of larva
developmental stage: 6 day post fertilization
Treatment protocol WT, zPer2 zCry1a double KO (DKO) , and zPer2 zCry1a zCry2a triple KO (TKO) zebrafish were kept in constant darkness after fertilization. They were then treated with light for 3- or 12-h at 6 dpf, or kept in constant darkness.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from zebrafish treated as described in figure legends using Trizol Reagent (Invitrogen). The quality of RNA was initially assessed by electrophoresis on a 1.5% agarose gel, and further by absorption spectrophotometry.
Label Cy3
Label protocol cDNAs were synthesized by the Low Input Quick Amp Labeling Kit. Cy3-labelled cRNA was synthesized by in vitro transcription with T7 RNA Polymerase.
 
Hybridization protocol RNA quality assurance, cDNA synthesis, and cRNA labeling and hybridization were carried out by Takara Bio Inc. (Otsu, Japan) using a Zebrafish (V3) Gene Expression Microarray 4X44K, the Low Input Quick Amp Labeling Kit, the Gene Expression Hybridization Kit, and the Gene Expression Wash Buffers Pack (all from Agilent Technologies) according to the manufacturer’s protocols.
Scan protocol Genechips scanned using an Agilent DNA Microarray Scanner (G2565CA)
Description Gene expression in TKO zebrafish exposed to 3-h light
Data processing Microarray data were processed using GeneChip Operating Software (Feature Extraction)
 
Submission date Mar 07, 2018
Last update date Feb 27, 2019
Contact name Jun Hirayama
E-mail(s) hirayama.dbio@mri.tmd.ac.jp
Organization name Tokyo Medical and Dental University
Department Medical Research Institute
Lab Department of Developmental and Regenerative Biology
Street address 1-5-45 Yushima, Bunkyo-ku
City Tokyo
ZIP/Postal code 113-8510
Country Japan
 
Platform ID GPL14688
Series (1)
GSE111521 Light-dependent expression profiles in WT, DKO, and TKO zebrafish

Data table header descriptions
ID_REF
VALUE processed

Data table
ID_REF VALUE
12 1043.79673
13 55.68943615
14 15.68395115
15 4.886332835
16 4457.02746
17 206.7775717
18 25.73765268
19 1060.088254
20 65165.65702
21 19.32749227
22 8789.913317
23 3114.686587
24 1023.894184
25 314.8981705
26 32.71989466
27 505.4722557
28 2733.439794
29 4482.556187
30 121.600037
31 305.6769229

Total number of rows: 43803

Table truncated, full table size 755 Kbytes.




Supplementary file Size Download File type/resource
GSM3032612_zPer2_zCry1a_zCry2a_triple_KO_3h_light.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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