Series Summary for DCD000171SR

Zic3 interacts with distant regulatory elements to regulate zebrafish developmental genes

Case Control

10.1371/journal.pgen.1003852

GSE41458

Zic3 regulates early embryonic patterning in vertebrates. Its loss-of-function disrupts gastrulation, left-right patterning, and neurogenesis. We use the zebrafish as a model to study the developmental role of Zic3 in vivo. Using a combination of two genomics approaches – ChIP-seq and microarray, we identified Zic3 targets, which include genes from the Nodal and Wnt pathways, and show for the first time cis-regulation of these genes by Zic3 using in vivo enhancer assay. We uncovered a previously unrecognized link between Zic3 and the non-canonical Wnt pathway in gastrulation and left-right patterning, and identified neural pre-pattern genes as Zic3 targets during the early steps of neural induction. Zic3 preferably binds to distal intergenic regions, some of which contain evolutionarily conserved functional enhancers.

True

cwinata

May 16, 2016, 8:07 a.m.

Nov. 7, 2018, 2:49 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Anatomical Term Hours Post Fertilization
DCD006320BS DCD000171SR whole organism Mathavan Lab, NTU Medical School AB 75%-epiboly 8
Applied Assay ID Biosample Replicate Assay
DCD000988AA DCD012444BR ChIP-seq_Mathavan_Lab_Zic3_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Chemistry Version Paired End Strand Sequencing Date
DCD000846SQ DCD000985TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 01/01/2012
DCD000551DT: FASTQ
DCD006365DT: LOG GRCz10/danRer10
DCD006369DT: LOG GRCz10/danRer10
DCD006370DT: BAM GRCz10/danRer10
DCD006371DT: LOG GRCz10/danRer10
DCD006372DT: LOG GRCz10/danRer10
DCD006374DT: PDF GRCz10/danRer10
DCD006375DT: LOG GRCz10/danRer10
DCD006377DT: BAM GRCz10/danRer10
DCD006378DT: BAM GRCz10/danRer10
DCD006382DT: BAM GRCz10/danRer10
DCD006390DT: BAM GRCz10/danRer10
DCD008949DT: BIGNARROWPEAK GRCz10/danRer10
DCD009053DT: BIGWIG GRCz10/danRer10
DCD016170DT: BAM GRCz11/danRer11
DCD016172DT: BED GRCz11/danRer11
DCD016173DT: BIGNARROWPEAK GRCz11/danRer11
DCD016174DT: BIGNARROWPEAK GRCz11/danRer11
DCD016177DT: BIGWIG GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD000983AA DCD012446BR ChIP-seq_Mathavan_Lab_input_control_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD000841SQ DCD000980TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 01/01/2012
DCD000546DT: FASTQ
DCD006311DT: LOG GRCz10/danRer10
DCD006313DT: LOG GRCz10/danRer10
DCD006314DT: BAM GRCz10/danRer10
DCD006316DT: LOG GRCz10/danRer10
DCD006317DT: LOG GRCz10/danRer10
DCD006318DT: BAM GRCz10/danRer10
DCD006319DT: PDF GRCz10/danRer10
DCD006320DT: LOG GRCz10/danRer10
DCD006323DT: BAM GRCz10/danRer10
DCD006329DT: BAM GRCz10/danRer10
DCD006333DT: BAM GRCz10/danRer10
DCD017009DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006321BS DCD000171SR tissue Mathavan Lab, NTU Medical School AB 26+ somites 24
Applied Assay ID Biosample Replicate Assay
DCD000990AA DCD012443BR ChIP-seq_Mathavan_Lab_Zic3_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD000848SQ DCD000987TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 01/01/2012
DCD000553DT: FASTQ
DCD006387DT: LOG GRCz10/danRer10
DCD006391DT: BAM GRCz10/danRer10
DCD006392DT: LOG GRCz10/danRer10
DCD006394DT: LOG GRCz10/danRer10
DCD006395DT: LOG GRCz10/danRer10
DCD006396DT: PDF GRCz10/danRer10
DCD006397DT: LOG GRCz10/danRer10
DCD006400DT: BAM GRCz10/danRer10
DCD006403DT: BAM GRCz10/danRer10
DCD006405DT: BAM GRCz10/danRer10
DCD006410DT: BAM GRCz10/danRer10
DCD008952DT: BIGNARROWPEAK GRCz10/danRer10
DCD009059DT: BIGWIG GRCz10/danRer10
DCD016241DT: BIGNARROWPEAK GRCz11/danRer11
DCD016242DT: BIGNARROWPEAK GRCz11/danRer11
DCD016243DT: BED GRCz11/danRer11
DCD016244DT: BIGWIG GRCz11/danRer11
DCD016245DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD000985AA DCD012445BR ChIP-seq_Mathavan_Lab_input_control_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD000843SQ DCD000982TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 01/01/2012
DCD000548DT: FASTQ
DCD006332DT: LOG GRCz10/danRer10
DCD006335DT: LOG GRCz10/danRer10
DCD006336DT: BAM GRCz10/danRer10
DCD006338DT: LOG GRCz10/danRer10
DCD006339DT: LOG GRCz10/danRer10
DCD006341DT: PDF GRCz10/danRer10
DCD006342DT: BAM GRCz10/danRer10
DCD006344DT: LOG GRCz10/danRer10
DCD006348DT: BAM GRCz10/danRer10
DCD006351DT: BAM GRCz10/danRer10
DCD006360DT: BAM GRCz10/danRer10
DCD016998DT: BAM GRCz11/danRer11