Series Summary for DCD000204SR

Genome-wide maps of binding sites of Nanog-like and Mxtx2 in blastula stage zebrafish embryos

Survey

10.1016/j.devcel.2012.01.003

GSE34683

Here, using ChIP-Seq, we examined the targets of Nanog-like and Mxtx2 in blastula stage zebrafish embryos. We found that Nanog-like bind to its known targets like Oct4, Sox2, and Nanog-like. Nanog-like also bound to genes involved in extraembryonic lineage differentiation, like gata3 and krt4 for EVL differentiation, and mxtx2 and slc26a1 for YSL differentiation, mesoderm specification like ntl and tbx3, cell movement like wnt11 and cxcr4b, and signaling genes like ndr1, bmp2b, fgf8a and wnt8a. The binding profile suggests that Nanog-like may play a versatile role involving many developmental processes. We found 11.3% of the genes (1751 out of all annotated 15500 zebrafish genes) and 43.6% of the YSL genes (118 out of 271 genes expressed in the YSL) were bound by Mxtx2, suggesting Mxtx2 bound directly to YSL genes to activate their expression

True

syang

June 2, 2016, 3:02 p.m.

Nov. 7, 2018, 2:54 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006555BS DCD000204SR whole organism Zon Lab, Boston Children's Hospital WT Oblong 3.5
Applied Assay ID Biosample Replicate Assay
DCD001252AA DCD012681BR ChIP-seq_Zon_Lab_Input_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001037SQ DCD001242TR Zon Lab, Boston Children's Hospital Illumina GAIIx 11/03/2010
DCD000653DT: FASTQ
DCD006453DT: LOG GRCz10/danRer10
DCD006456DT: LOG GRCz10/danRer10
DCD006457DT: BAM GRCz10/danRer10
DCD006459DT: LOG GRCz10/danRer10
DCD006460DT: LOG GRCz10/danRer10
DCD006461DT: BAM GRCz10/danRer10
DCD006462DT: PDF GRCz10/danRer10
DCD006463DT: LOG GRCz10/danRer10
DCD006469DT: BAM GRCz10/danRer10
DCD006471DT: BAM GRCz10/danRer10
DCD006475DT: BAM GRCz10/danRer10
DCD017012DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001253AA DCD012681BR ChIP-seq_Zon_Lab_nanog-like_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001035SQ DCD001234TR Zon Lab, Boston Children's Hospital Illumina GAIIx 11/03/2010
DCD000655DT: FASTQ
DCD006465DT: LOG GRCz10/danRer10
DCD006467DT: LOG GRCz10/danRer10
DCD006468DT: BAM GRCz10/danRer10
DCD006470DT: LOG GRCz10/danRer10
DCD006472DT: LOG GRCz10/danRer10
DCD006473DT: PDF GRCz10/danRer10
DCD006474DT: LOG GRCz10/danRer10
DCD006477DT: BAM GRCz10/danRer10
DCD006478DT: BAM GRCz10/danRer10
DCD006488DT: BAM GRCz10/danRer10
DCD006494DT: BAM GRCz10/danRer10
DCD009002DT: BIGNARROWPEAK GRCz10/danRer10
DCD009115DT: BIGWIG GRCz10/danRer10
DCD016205DT: BIGNARROWPEAK GRCz11/danRer11
DCD016206DT: BIGNARROWPEAK GRCz11/danRer11
DCD016207DT: BED GRCz11/danRer11
DCD016208DT: BAM GRCz11/danRer11
DCD016213DT: BIGWIG GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006556BS DCD000204SR whole organism Zon Lab, Boston Children's Hospital WT 30%-epiboly 4.5
Applied Assay ID Biosample Replicate Assay
DCD001229AA DCD012680BR ChIP-seq_Zon_Lab_Mxtx2_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001026SQ DCD001257TR Zon Lab, Boston Children's Hospital Illumina GAIIx 11/03/2010
DCD000648DT: FASTQ
DCD006420DT: LOG GRCz10/danRer10
DCD006423DT: LOG GRCz10/danRer10
DCD006424DT: BAM GRCz10/danRer10
DCD006426DT: LOG GRCz10/danRer10
DCD006427DT: LOG GRCz10/danRer10
DCD006428DT: BAM GRCz10/danRer10
DCD006429DT: PDF GRCz10/danRer10
DCD006430DT: LOG GRCz10/danRer10
DCD006433DT: BAM GRCz10/danRer10
DCD006439DT: BAM GRCz10/danRer10
DCD006440DT: BAM GRCz10/danRer10
DCD009000DT: BIGNARROWPEAK GRCz10/danRer10
DCD009116DT: BIGWIG GRCz10/danRer10
DCD016266DT: BAM GRCz11/danRer11
DCD016267DT: BIGNARROWPEAK GRCz11/danRer11
DCD016268DT: BIGNARROWPEAK GRCz11/danRer11
DCD016269DT: BED GRCz11/danRer11
DCD016273DT: BIGWIG GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001230AA DCD012680BR ChIP-seq_Zon_Lab_Input_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001012SQ DCD001259TR Zon Lab, Boston Children's Hospital Illumina GAIIx 11/03/2010
DCD000647DT: FASTQ
DCD006409DT: LOG GRCz10/danRer10
DCD006412DT: LOG GRCz10/danRer10
DCD006413DT: BAM GRCz10/danRer10
DCD006416DT: LOG GRCz10/danRer10
DCD006417DT: LOG GRCz10/danRer10
DCD006418DT: PDF GRCz10/danRer10
DCD006419DT: LOG GRCz10/danRer10
DCD006421DT: BAM GRCz10/danRer10
DCD006422DT: BAM GRCz10/danRer10
DCD006425DT: BAM GRCz10/danRer10
DCD006436DT: BAM GRCz10/danRer10
DCD017005DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001231AA DCD012683BR ChIP-seq_Zon_Lab_nanog-like_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD001021SQ DCD001244TR Zon Lab, Boston Children's Hospital Illumina GAIIx 07/28/2010
DCD000652DT: FASTQ
DCD006442DT: LOG GRCz10/danRer10
DCD006445DT: LOG GRCz10/danRer10
DCD006446DT: BAM GRCz10/danRer10
DCD006447DT: BAM GRCz10/danRer10
DCD006448DT: LOG GRCz10/danRer10
DCD006450DT: LOG GRCz10/danRer10
DCD006451DT: PDF GRCz10/danRer10
DCD006452DT: LOG GRCz10/danRer10
DCD006455DT: BAM GRCz10/danRer10
DCD006458DT: BAM GRCz10/danRer10
DCD006466DT: BAM GRCz10/danRer10
DCD009001DT: BIGNARROWPEAK GRCz10/danRer10
DCD009117DT: BIGWIG GRCz10/danRer10
DCD016131DT: BIGNARROWPEAK GRCz11/danRer11
DCD016132DT: BED GRCz11/danRer11
DCD016133DT: BIGNARROWPEAK GRCz11/danRer11
DCD016134DT: BAM GRCz11/danRer11
DCD016135DT: BIGWIG GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001232AA DCD012683BR ChIP-seq_Zon_Lab_Input_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001036SQ DCD001252TR Zon Lab, Boston Children's Hospital Illumina GAIIx 07/28/2010
DCD000649DT: FASTQ
DCD006431DT: LOG GRCz10/danRer10
DCD006434DT: LOG GRCz10/danRer10
DCD006435DT: BAM GRCz10/danRer10
DCD006437DT: LOG GRCz10/danRer10
DCD006438DT: LOG GRCz10/danRer10
DCD006441DT: LOG GRCz10/danRer10
DCD006443DT: PDF GRCz10/danRer10
DCD006444DT: BAM GRCz10/danRer10
DCD006449DT: BAM GRCz10/danRer10
DCD006454DT: BAM GRCz10/danRer10
DCD006464DT: BAM GRCz10/danRer10
DCD017023DT: BAM GRCz11/danRer11