Dataset Information

Mus musculus strain:Shox2-HA

ABSTRACT: Mus musculus strain:Shox2-HA Raw sequence reads

PROVIDER: PRJNA287463 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	SRR2079841.fastq.gz	Fastqsanger.gz
	SRR2075772.fastq.gz	Fastqsanger.gz
	SRR2075773.fastq.gz	Fastqsanger.gz
	SRR2075774.fastq.gz	Fastqsanger.gz
	SRR2079537.fastq.gz	Fastqsanger.gz

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Project description:ChIP-Sequencing on Shox2-HA E12.5 and E13.5 Limb and Palate, as well as Pbx on E12.5 limb . Abstract: Vertebrate appendage patterning is programmed by Hox-TALE factors-bound regulatory elements. However, it remains enigmatic which cell lineages are commissioned by Hox-TALE factors to generate regional specific pattern and whether other Hox-TALE co-factors exist. In this study, we investigated the transcriptional mechanisms controlled by the Shox2 transcriptional regulator in limb patterning. Harnessing an osteogenic lineage-specific Shox2 inactivation approach we show that despite widespread Shox2 expression in multiple cell lineages, lack of the stylopod observed upon Shox2 deficiency is a specific result of Shox2 loss of function in the osteogenic lineage. ChIP-Seq revealed robust interaction of Shox2 with cis-regulatory enhancers clustering around skeletogenic genes that are also bound by Hox-TALE factors, supporting a lineage autonomous function of Shox2 in osteogenic lineage fate determination and skeleton patterning. Pbx ChIP-Seq further allowed the genome-wide identification of cis-regulatory modules exhibiting co-occupancy of Pbx, Meis, and Shox2 transcriptional regulators. Integrative analysis of ChIP-Seq and RNA-Seq data and transgenic enhancer assays indicate that Shox2 patterns the stylopod as a repressor via interaction with enhancers active in the proximal limb mesenchyme and antagonizes the repressive function of TALE factors in osteogenesis. Shox2/TALE For ChIP-Seq, the list of libraries below, including controls, were generated [listed in the format of (antibody)-target-tissue-stage]: (Î±-HA)-Shox2-Limb-E12.5, (Î±-HA)-Shox2-Limb-E13.5, (Î±-HA)-Shox2-Palate-E12.5, (Î±-HA)-Shox2-Limb/Palate-E12.5, (Î±-Pbx)-Pbx-Limb-E12.5, Input (control), (Î±-HA)-Mixed Limb/Palate from Shox2+/+ mice-E12.5 (control). *The attached signal tracks(*.bigwig) were generated by âbdgcmp (MACS2) to filter out background signal(by filtering against the signal track obtained from (Î±-HA)-Mixed Limb/Palate from Shox2+/+ mice-E12.5 (control)) and subsequently convert to bigwig for analysis and visualization.

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Mus musculus strain:Shox2-HA

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