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Sample GSM440814 Query DataSets for GSM440814
Status Public on Mar 01, 2010
Title MZ at 5 hpf replicate 2
Sample type RNA
 
Source name MZ whole embryo
Organism Danio rerio
Characteristics hours post fertilization: 5
stage: 40% epiboly
Treatment protocol Embryos of the genotypes indicated were precisely staged either following in vitro fertilization (t=0 hpf), or using natural crosses and staging at the 4-cell stage (t=1 hpf)
Growth protocol WT embryos of AB x TÜB strain crosses (www.ZFIN.org) and MZ embryos carrying the m793 allele of the spg mutation were used
Extracted molecule total RNA
Extraction protocol 60-100 embryos per sample were snap-frozen in liquid nitrogen, and total RNA was isolated using the RNA Easy kit (Qiagen). Sample quality was assessed in an Agilent Bioanalyzer 2100, using the RNA 6000 nano Assay Kit
Label Cy5
Label protocol Samples were processed by Agilent Technologies Two-Color Microarray-Based Gene Expression Analysis kit according to Agilent Two-color Microarray based gene expression analysis protocol
 
Hybridization protocol Agilent Gene Expression Hybridization Kit was used . Micorarrays were hybridized in the Agilent 2545A hybridization oven according Agilent Two-color Microarray based gene expression analysis protocol
Scan protocol Scanned on an Agilent G2565AA scanner
Description MZ to WT comparison 40p Replicate 2
Data processing Data were extracted using Agilent Feature Extraction Software and GE2-v5_95_Feb07 protocoll.
 
Submission date Aug 14, 2009
Last update date Feb 06, 2023
Contact name Daria Onichtchouk
E-mail(s) daria.onichtchouk@biologie.uni-freiburg.de
Phone 00497612032595
Organization name University of Freiburg
Street address Hauptstrasse 1
City Freiburg
ZIP/Postal code 79104
Country Germany
 
Platform ID GPL7302
Series (2)
GSE17655 Experiment 1: Developmental time curve in wild-type and MZspg embryos
GSE17667 Pou5f1 transcription targets in zebrafish

Data table header descriptions
ID_REF
VALUE Further Normalisation and processing of the data was done using Genedata Expressionist and Analyst software. Cy3 and Cy5 channels of each microarray were normalized using quantile mormalization

Data table
ID_REF VALUE
GE_BrightCorner 5498.504
DarkCorner 5.049813
A_15_P119205 7199.386
A_15_P111700 2405.507
A_15_P104358 20.25045
A_15_P100254 5.819374
A_15_P116237 4.822147
A_15_P105104 6.085169
A_15_P100012 6507.342
A_15_P106735 54.7785
A_15_P103037 4.967322
A_15_P101834 393.5863
A_15_P110751 379.4796
A_15_P112178 5.326921
A_15_P119305 149.413
A_15_P106450 5.371455
A_15_P105607 3.946243
A_15_P109489 2604.161
A_15_P103593 27.30939
A_15_P111179 212.2334

Total number of rows: 21539

Table truncated, full table size 459 Kbytes.




Supplementary file Size Download File type/resource
GSM440814_US45103001_251506410447_S01_GE2-v5_95_Feb07_1_4_40percentepiboly_R2_39.txt.gz 13.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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