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Series GSE18830 Query DataSets for GSE18830
Status Public on Dec 31, 2009
Title B1 sox (sox2/3/19a/19b) quadruple knockdown in the zebrafish embryo
Organism Danio rerio
Experiment type Expression profiling by array
Summary The B1 SOX transcription factors SOX1/2/3/19 have been implicated in various processes of early embryogenesis. However, their regulatory functions in stages from the blastula to early neurula remain largely unknown, primarily because loss-of-function studies have not been informative to date. In our present study, we systematically knocked down the B1 sox genes in zebrafish. Only the quadruple knockdown of the four B1 sox genes sox2/3/19a/19b, which are active in the early embryo, resulted in very severe developmental abnormalities, confirming that the B1 sox genes are functionally redundant. We characterized the sox2/3/19a/19b quadruple knockdown embryos in detail by examining the changes in gene expression through microarray analysis as well as in situ hybridization.
Importantly, these phenotypic analyses of the quadruple knockdown embryos reveled that the B1 SOX proteins regulate the following distinct processes: (1) early dorsoventral patterning by controlling bmp2b/7; (2) gastrulation movements via the regulation of pcdh18a/18b and non-canonical wnt genes; (3) neural differentiation by regulating the Hes-class bHLH gene her3 and the proneural-class bHLH genes neurog1 (positively) and ascl1a (negatively), and regional transcription factor genes, e.g. hesx1, zic1 and rx3; and (4) neural patterning by regulating signaling pathway genes, cyp26a1 in RA signaling, oep in Nodal signaling, shh, and mdkb. These findings indicate that the B1 SOX proteins control a wide range of developmental regulators in the early embryo and suggest that the B1 sox functions are central to coordinating cell fate specification with patterning and morphogenetic processes occurring in the early embryo.
 
Overall design Microarray analysis was carried out to compare gene expression profiles at the 30% epiboly (30%E), 75% epiboly (75%E) and tailbud (TB) stages between wild-type embryos and the sox2/3/19a/19b quadruple knockdown embryos. RNAs from two independent samples were analyzed for each embryonic stage.
 
Contributor(s) Okuda Y, Kamachi Y
Citation(s) 20463883
Submission date Oct 30, 2009
Last update date Jan 25, 2018
Contact name Yusuke Kamachi
E-mail(s) yusuke@fbs.osaka-u.ac.jp
Organization name Osaka University
Department Graduate School of Frontier Biosciences
Street address 1-3 Yamadaoka
City Suita
State/province Osaka
ZIP/Postal code 565-0871
Country Japan
 
Platforms (1)
GPL1319 [Zebrafish] Affymetrix Zebrafish Genome Array
Samples (12)
GSM466790 Zebrafish wt embryo_ 30%E_biological rep1
GSM466791 Zebrafish wt embryo_ 30%E_biological rep2
GSM466792 Zebrafish wt embryo_ 75%E_biological rep1
Relations
BioProject PRJNA121165

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE18830_RAW.tar 23.1 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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