Return to search results Title: Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula

Summary

RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. Here we present a deep RNA-seq dataset of transcripts expressed in dorsal and ventral lips of the early Xenopus gastrula embryo using the new genomic information, which was further annotated by blast searches against the human proteome. Overall, our findings confirm previous results from differential screenings using other methods that uncovered classical dorsal genes such as Chordin, Noggin and Cerberus, as well as ventral genes such as Sizzled, Ventx, Wnt8 and BAMBI. Complete transcriptome-wide Excel files of mRNAs suitable for data mining are presented, which include many novel dorsal- and ventral-specific genes. RNA-seq was very quantitative and reproducible, and allowed us to define dorsal and ventral signatures useful for gene set expression analyses (GSEA). As an example of a new gene, we present here data on an organizer-specific secreted protein tyrosine kinase known as Pkdcc (protein kinase domain containing, cytoplasmic) or Vlk (vertebrate lonesome kinase). Overexpression experiments indicate that Pkdcc can act as a negative regulator of Wnt/ β-catenin signaling independently of its kinase activity. We conclude that RNA-seq in combination with the Xenopus laevis complete genome now available provides a powerful tool for unraveling cell-cell signaling pathways during embryonic induction.

Contributors: Edward De Robertis, Yi Ding, Gabriele Colozza, Kelvin Zhang, Yuki Moriyama, Diego Ploper, Eric Sosa, Maria Benitez

Experiment Type: One stage 10.5 wild type whole embryo and triplicates of stage 10.5 dorsal lips and ventral lips are sequenced.

Article: XB-ART-51980, PubMed

Source: NCBI GEO, Xenbase Download

Sample	View		GSMs	Assay Type
WE - NF10.5 GSM1948717  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10.5      lower blastopore lip - NF10.5 DEG GSM1948719  GSM1948721  GSM1948723  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody lower blastopore lip NF stage 10.5      upper blastopore lip - NF10.5 DEG GSM1948718  GSM1948720  GSM1948722  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody upper blastopore lip NF stage 10.5

Select All DEG

Select All  Xtr    Xla

Return to search results