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Single cell Chromatin Accessibility profiling of forelimb bud at stage E11.5 in WT and Hox13 mutant (10x Chromium)

ABSTRACT: Single cell Chromatin Accessibility profiling of forelimb bud at stage E11.5 in WT and Hox13 mutant (10x Chromium)

PROVIDER: PRJNA607966 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11139144_1.fastq.gz	Fastqsanger.gz
	SRR11139144_2.fastq.gz	Fastqsanger.gz
	SRR11139145_1.fastq.gz	Fastqsanger.gz
	SRR11139145_2.fastq.gz	Fastqsanger.gz

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Single cell Chromatin Accessibility profiling of forelimb bud at stage E11.5 in WT and Hox13 mutant (10x Chromium)

Project description:Single cell Chromatin Accessibility profiling of forelimb bud at stage E11.5 in WT and Hox13 mutant (10x Chromium)

2020-03-26 | GSE145657 | GEO

Variant PRC1 competes with retinoic acid-related signals to repress Meis2 in distal forelimb bud

Project description:Suppression of Meis genes in the distal limb bud is required for Proximal-Distal (PD) specification of the forelimb. Polycomb group (PcG) factors play a role in downregulation of retinoic acid (RA)-related signals in the distal forelimb bud, causing Meis repression. It is, however, not known if downregulation of RA-related signals and PcG-mediated proximal genes repression are functionally linked. Here, we reveal that PcG factors and RA-related signals antagonize each other to polarize Meis2 expression along the PD axis. With mathematical modeling and simulation, we propose that PcG factors are required to adjust the threshold for RA-related signaling to regulate Meis2 expression. Finally, we show that a variant Polycomb repressive complex 1 (PRC1), incorporating PCGF3 and PCGF5, represses Meis2 expression in the distal limb bud. Taken together, we reveal a previously unknown link between PcG proteins and downregulation of RA-related signals to mediate the phase transition of Meis2 transcriptional status during forelimb patterning.

2018-09-07 | GSE105206 | GEO

H3K4me1 & H3K27ac ChIP on chip for Mouse E11.5 distal limb bud tissue

Project description:Profiling H3K4me1 & H3K27ac histone modifications across the ZRS and a selection of limb development genes within Mouse E11.5 distal limb bud tissue.

2018-01-01 | GSE104074 | GEO

RING1 links retinoic acid signaling to the early proximal-distal specification of forelimb bud via Meis2 repression (mRNA)

Project description:Polycomb group (PcG) proteins play a pivotal role in silencing of development-related genes and contribute to maintain various stem and precursor cells and regulate their differentiation. However, it is not well understood how PcG factors regulate dynamic and complex morphogenetic processes particularly in mammals. In this study, we focused on proximal-distal (PD) patterning of forelimb bud to elucidate how PcG factors contribute to regulation of morphogenetic processes that depends on developmental signals. Depletion of RING1 proteins, which are common components of both canonical and variant Polycomb repressive complex-1 (PRC1), led to dramatic deficiencies in forelimb formation. By using Ring1-deficient forelimb buds, we revealed the early defects in distal specification, which is due to the functional coupling of RING1 and retinoic acid (RA) signaling. RING1 activity is shown to antagonize with RA signals at Meis2 and likely Meis1, which are superior suppressors of distal formation program, in the prospective distal region of outgrowing forelimb bud. This study exhibits a first example showing how PcG factors interplay with developmental signals to mediate compartmentalization of elongating anlagen by regulating the expression of developmental genes.

2015-12-28 | GSE70075 | GEO

RING1 links retinoic acid signaling to the early proximal-distal specification of forelimb bud via Meis2 repression (ChIP-Seq)

2015-12-28 | GSE70076 | GEO

RING1 links retinoic acid signaling to the early proximal-distal specification of forelimb bud via Meis2 repression (ChIP-chip)

2015-12-28 | GSE70074 | GEO

RING1 proteins contribute to early proximal-distal specification of the forelimb bud by restricting Meis2 expression

Project description:Polycomb group (PcG) proteins play a pivotal role in silencing developmental genes and help to maintain various stem and precursor cells and regulate their differentiation. PcG factors also regulate dynamic and complex regional specification, particularly in mammals, but this activity is mechanistically not well understood. In this study, we focused on proximal-distal (PD) patterning of the mouse forelimb bud to elucidate how PcG factors contribute to a regional specification process that depends on developmental signals. Depletion of the RING1 proteins RING1A (RING1) and RING1B (RNF2), which are essential components of Polycomb repressive complex 1 (PRC1), led to severe defects in forelimb formation along the PD axis. We show that preferential defects in early distal specification in Ring1A/B-deficient forelimb buds accompany failures in the repression of proximal signal circuitry bound by RING1B, including Meis1/2, and the activation of distal signal circuitry in the prospective distal region. Additional deletion of Meis2 induced partial restoration of the distal gene expression and limb formation seen in the Ring1A/B-deficient mice, suggesting a crucial role for RING1-dependent repression of Meis2 and likely also Meis1 for distal specification. We suggest that the RING1-MEIS1/2 axis is regulated by early PD signals and contributes to the initiation or maintenance of the distal signal circuitry. This SuperSeries is composed of the SubSeries listed below.

2015-12-28 | GSE70077 | GEO

Comparative transcriptomic analyssi of mouse embryonic tissues and mESCs-derived limb bud-organoid tissues

Project description:We established the differentiation method of a limb bud organoid from mouse embryonic stem cells (mESCs) using SFEBq. mESCs-derived limb bud organoid selectively differentiate into forelimb or hindlimb by adjusting the retinoic acids activity. To evaluate a correlation of gene expression between limb bud organoid and embryonic tissues (limb bud, branchial arch, cardiac, and tail bud), we performed comparative transcriptome analysis using RNA-seq.

2019-05-01 | GSE126387 | GEO

Complete embryonic E11.5 metanephric kidney analysis of wild type and Hoxa11, Hoxd11 null targeted mice

Project description:E11.5 metanephric mesenchyme and ureteric bud were dissected from the E11.5 kidney rudiment using fine manual microdissection (ureteric bud only) or both fine manual microdissection and laser capture microdissection (metanephric mesenchyme) to define the gene expression profiles of these structures. Additionally, HoxA11, HoxD11 compound null E11.5 metanephric mesenchyme was obtained through laser capture microdissection allowing analysis of possible Hox targets in kidney development. Targets from multiple biological replicates of each were generated and the expression profiles were determined using Affymetrix MOE430_v2 arrays. Keywords: embryonic metanephric kidney, kidney development, Hoxa11, Hoxd11, compound null targeted mice

2006-05-01 | GSE3822 | GEO

H3K4me1 & H3K27ac ChIP on chip for Mouse E11.5 distal limb bud tissue

Project description:H3K4me1 & H3K27ac ChIP on chip for Mouse E11.5 distal limb bud tissue

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