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Sample GSM440867 Query DataSets for GSM440867
Status Public on Mar 01, 2010
Title WT CHX treated replicate 2
Sample type RNA
 
Source name WT whole embryo
Organism Danio rerio
Characteristics hours post fertilization: 4.7
cycloheximide treatment at 1,5 hpf: YES
microinjection: NO
Treatment protocol Embryos of the genotypes indicated were injected with 100 pg/embryo Pou5f1 mRNA, 50 pg/embryo Sox2 mRNA or left uninjected. At 1,5 hpf, the embryos were placed into 15 mkg/ml Cycloheximide solution (Calbiochem), until the embryos were frozen for RNA isolation
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 Cy3
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 protocoll
 
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 protocoll
Scan protocol Scanned on an Agilent G2565AA scanner
Description WT CHX treated 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)
GSE17659 Experiment 2: Pou5f1 and Sox2 overexpression experiments with or without protein synthesis inhibition
GSE17667 Pou5f1 transcription targets in zebrafish
Relations
Reanalyzed by GSM1008632

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. Quantie normalization was separately applied to Samples S-60 to S-65 and to S-66 to

Data table
ID_REF VALUE
GE_BrightCorner 1260.442
DarkCorner 3.791853
A_15_P119205 6296.417
A_15_P111700 1286.586
A_15_P104358 25.67107
A_15_P100254 7.220174
A_15_P116237 3.853491
A_15_P105104 8.791532
A_15_P100012 7638.023
A_15_P106735 831.9069
A_15_P103037 5.805507
A_15_P101834 1515.445
A_15_P110751 619.7218
A_15_P112178 3.90996
A_15_P119305 181.3292
A_15_P106450 5.772693
A_15_P105607 6.513636
A_15_P109489 2361.062
A_15_P103593 7.681615
A_15_P111179 269.5504

Total number of rows: 21535

Table truncated, full table size 457 Kbytes.




Supplementary file Size Download File type/resource
GSM440867_PCRstudy_251506410375_S01_Cropped_GE2-v5_95_zeb_3_1_2_8.txt.gz 14.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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