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Series GSE106430 Query DataSets for GSE106430
Status Public on Aug 15, 2018
Title Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [RNA-Seq]
Organisms Branchiostoma lanceolatum; Danio rerio; Oryzias latipes
Experiment type Expression profiling by high throughput sequencing
Summary What genomic changes led to the origin of vertebrates remains a mystery. On the one hand, animal evolution is thought to be driven mostly by changes in the cis-regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand, vertebrates experienced two rounds of whole genome duplication (WGD) that increased their gene repertoire, particularly of regulatory genes controlling embryo development. To shed light into the origin and evolution of the vertebrate regulatory genome, we have generated an unprecedented transcriptomic and epigenomic resource for the non-duplicated genome of the European amphioxus, a closely related invertebrate chordate. These data include RNA-seq for more than 35 developmental stages and adult tissues, CAGE-seq, ChIP-seq, bisulphite-seq and ATAC-seq for several developmental stages and adult tissues. By comparing these data sets with equivalent novel and previously available data for various vertebrate species, especially zebrafish, we uncovered multiple conserved and vertebrate-specific regulatory landmarks. We first identify a conserved chordate phylotypic stage, a developmental period in which different chordate species show the highest gene expression similarity. We also shed light on the origin of enhancer demethylation in vertebrates, by identifying, for the first time in an invertebrate species, differentially methylated enhancers. Furthermore, we show that conserved clusters of co-expressed and tissue-specific genes display similar enrichments for cis-regulatory motifs between amphioxus and vertebrates. Finally, we study the impact of vertebrate WGDs on the evolution of gene regulation, providing the first genome-wide quantitative assessment of sub-functionalization and neo-functionalization processes after the vertebrate WGDs; changing the way in which these evolutionary mechanisms have been traditionally understood.
 
Overall design RNA-seq assays in different developmental stages of european amphioxus, zebrafish and medaka
 
Contributor(s) Permanyer J, Burguera D, Escriva H, Bertrand S, Buono L, Martínez-Morales JR, Irimia M
Citation(s) 30464347
Submission date Nov 02, 2017
Last update date Nov 25, 2018
Contact name Juan J. Tena
E-mail jjtenagu@upo.es
Organization name CABD/CSIC
Street address Univ. Pablo Olavide, Ctra. Utrera km1
City Sevilla
ZIP/Postal code 41013
Country Spain
 
Platforms (4)
GPL18413 Illumina HiSeq 2500 (Danio rerio)
GPL20177 Illumina HiSeq 2000 (Branchiostoma lanceolatum)
GPL24206 Illumina HiSeq 2500 (Branchiostoma lanceolatum)
Samples (81)
GSM2837516 RNAseq amphioxus 10h replicate 1
GSM2837517 RNAseq amphioxus 10h replicate 2
GSM2837518 RNAseq amphioxus 11h replicate 1
This SubSeries is part of SuperSeries:
GSE106431 Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits
Relations
BioProject PRJNA416866
SRA SRP123447

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
GSE106430_Olat_bygene_kallisto_tpms.txt.gz 1.3 Mb (ftp)(http) TXT
GSE106430_RAW.tar 12.3 Mb (http)(custom) TAR (of TXT)
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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