Series Summary for DCD000205SR

A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis

Survey

10.1016/j.stemcr.2013.10.001

GSE48254

Deletion of caudal/cdx genes alters hox gene expression and causes defects in posterior tissues and hematopoiesis. Yet, the defects in hox gene expression only partially explain these phenotypes. To gain deeper insight into Cdx4 function, we performed ChIP-seq combined with gene expression profiling in zebrafish, and identified the transcription factor spalt-like 4 (sall4) as a Cdx4 target. ChIP-seq revealed that Sall4 bound to its own gene locus and the cdx4 locus. Expression profiling showed that Cdx4 and Sall4 co-regulate genes such as hox, scl, and lmo2 that initiate hematopoiesis. Combined cdx4/sall4 gene knock-down impairs erythropoiesis, and overexpression of the Cdx4 and Sall4 target genes scl and lmo2 together rescued the erythroid program. These findings suggest that auto- and cross- regulation of Cdx4 and Sall4 establish a stable molecular circuit in mesoderm that facilitates the activation of the blood-specific program as development proceeds.

True

syang

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

Nov. 7, 2018, 3 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background
DCD006562BS DCD000205SR whole organism Zon Lab, Boston Children's Hospital TU
Applied Assay ID Biosample Replicate Assay
DCD001242AA DCD012675BR ChIP-seq_Zon_Lab_Cdx4_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001030SQ DCD001249TR Zon Lab, Boston Children's Hospital Illumina GAIIx 09/14/2011
DCD000707DT: FASTQ
DCD006585DT: LOG GRCz10/danRer10
DCD006588DT: LOG GRCz10/danRer10
DCD006589DT: BAM GRCz10/danRer10
DCD006591DT: LOG GRCz10/danRer10
DCD006592DT: LOG GRCz10/danRer10
DCD006593DT: BAM GRCz10/danRer10
DCD006594DT: PDF GRCz10/danRer10
DCD006595DT: LOG GRCz10/danRer10
DCD006598DT: BAM GRCz10/danRer10
DCD006604DT: BAM GRCz10/danRer10
DCD006608DT: BAM GRCz10/danRer10
DCD008995DT: BIGNARROWPEAK GRCz10/danRer10
DCD009111DT: BIGWIG GRCz10/danRer10
DCD016344DT: BED GRCz11/danRer11
DCD016346DT: BAM GRCz11/danRer11
DCD016347DT: BIGNARROWPEAK GRCz11/danRer11
DCD016348DT: BIGNARROWPEAK GRCz11/danRer11
DCD016349DT: BIGWIG GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001239AA DCD012676BR ChIP-seq_Zon_Lab_Sall4_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001015SQ DCD001246TR Zon Lab, Boston Children's Hospital Illumina GAIIx 09/14/2011
DCD000703DT: FASTQ
DCD006574DT: LOG GRCz10/danRer10
DCD006577DT: LOG GRCz10/danRer10
DCD006578DT: BAM GRCz10/danRer10
DCD006580DT: LOG GRCz10/danRer10
DCD006582DT: LOG GRCz10/danRer10
DCD006583DT: PDF GRCz10/danRer10
DCD006584DT: LOG GRCz10/danRer10
DCD006587DT: BAM GRCz10/danRer10
DCD006590DT: BAM GRCz10/danRer10
DCD006596DT: BAM GRCz10/danRer10
DCD006599DT: BAM GRCz10/danRer10
DCD009118DT: BIGWIG GRCz10/danRer10
DCD016495DT: BIGNARROWPEAK GRCz11/danRer11
DCD016496DT: BIGNARROWPEAK GRCz11/danRer11
DCD016497DT: BED GRCz11/danRer11
DCD016498DT: BAM GRCz11/danRer11
DCD016501DT: BIGWIG GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001240AA DCD012678BR ChIP-seq_Zon_Lab_H3K27Ac_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001011SQ DCD001247TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2000 12/16/2011
DCD000701DT: FASTQ
DCD006564DT: LOG GRCz10/danRer10
DCD006566DT: LOG GRCz10/danRer10
DCD006567DT: BAM GRCz10/danRer10
DCD006569DT: LOG GRCz10/danRer10
DCD006570DT: LOG GRCz10/danRer10
DCD006572DT: PDF GRCz10/danRer10
DCD006573DT: LOG GRCz10/danRer10
DCD006576DT: BAM GRCz10/danRer10
DCD006579DT: BAM GRCz10/danRer10
DCD006581DT: BAM GRCz10/danRer10
DCD006586DT: BAM GRCz10/danRer10
DCD008990DT: BIGNARROWPEAK GRCz10/danRer10
DCD009108DT: BIGWIG GRCz10/danRer10
DCD016458DT: BIGNARROWPEAK GRCz11/danRer11
DCD016459DT: BIGNARROWPEAK GRCz11/danRer11
DCD016460DT: BED GRCz11/danRer11
DCD016461DT: BIGWIG GRCz11/danRer11
DCD016462DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001237AA DCD012685BR ChIP-seq_Zon_Lab_H3K4me3_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001005SQ DCD001237TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2000 12/16/2011
DCD000699DT: FASTQ
DCD006552DT: LOG GRCz10/danRer10
DCD006555DT: LOG GRCz10/danRer10
DCD006556DT: BAM GRCz10/danRer10
DCD006558DT: LOG GRCz10/danRer10
DCD006559DT: LOG GRCz10/danRer10
DCD006560DT: BAM GRCz10/danRer10
DCD006561DT: BAM GRCz10/danRer10
DCD006562DT: PDF GRCz10/danRer10
DCD006563DT: LOG GRCz10/danRer10
DCD006565DT: BAM GRCz10/danRer10
DCD006571DT: BAM GRCz10/danRer10
DCD008997DT: BIGNARROWPEAK GRCz10/danRer10
DCD009113DT: BIGWIG GRCz10/danRer10
DCD016277DT: BIGNARROWPEAK GRCz11/danRer11
DCD016278DT: BIGNARROWPEAK GRCz11/danRer11
DCD016279DT: BED GRCz11/danRer11
DCD016280DT: BAM GRCz11/danRer11
DCD016281DT: BIGWIG GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001238AA DCD012688BR ChIP-seq_Zon_Lab_Input_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001025SQ DCD001261TR Zon Lab, Boston Children's Hospital Illumina GAIIx 09/14/2011
DCD000696DT: FASTQ
DCD006542DT: LOG GRCz10/danRer10
DCD006544DT: LOG GRCz10/danRer10
DCD006545DT: BAM GRCz10/danRer10
DCD006548DT: LOG GRCz10/danRer10
DCD006549DT: LOG GRCz10/danRer10
DCD006550DT: PDF GRCz10/danRer10
DCD006551DT: LOG GRCz10/danRer10
DCD006554DT: BAM GRCz10/danRer10
DCD006557DT: BAM GRCz10/danRer10
DCD006568DT: BAM GRCz10/danRer10
DCD006575DT: BAM GRCz10/danRer10
DCD017039DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001236AA DCD012689BR ChIP-seq_Zon_Lab_Input_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001031SQ DCD001235TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2000 05/24/2013
DCD000690DT: FASTQ
DCD006520DT: LOG GRCz10/danRer10
DCD006522DT: LOG GRCz10/danRer10
DCD006523DT: BAM GRCz10/danRer10
DCD006525DT: LOG GRCz10/danRer10
DCD006526DT: LOG GRCz10/danRer10
DCD006528DT: PDF GRCz10/danRer10
DCD006529DT: LOG GRCz10/danRer10
DCD006539DT: BAM GRCz10/danRer10
DCD006543DT: BAM GRCz10/danRer10
DCD006547DT: BAM GRCz10/danRer10
DCD006553DT: BAM GRCz10/danRer10
DCD017026DT: BAM GRCz11/danRer11
Applied Assay ID Biosample Replicate Assay
DCD001235AA DCD012690BR ChIP-seq_Zon_Lab_Input_0003AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001008SQ DCD001250TR Zon Lab, Boston Children's Hospital Illumina HiSeq 2000 12/16/2011
DCD000693DT: FASTQ
DCD006531DT: LOG GRCz10/danRer10
DCD006532DT: BAM GRCz10/danRer10
DCD006533DT: LOG GRCz10/danRer10
DCD006534DT: BAM GRCz10/danRer10
DCD006535DT: BAM GRCz10/danRer10
DCD006536DT: LOG GRCz10/danRer10
DCD006537DT: LOG GRCz10/danRer10
DCD006538DT: BAM GRCz10/danRer10
DCD006540DT: PDF GRCz10/danRer10
DCD006541DT: LOG GRCz10/danRer10
DCD006546DT: BAM GRCz10/danRer10
DCD016999DT: BAM GRCz11/danRer11