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

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

ORGANISM(S): Mus musculus

PROVIDER: GSE104074 | GEO | 2018/01/01

SECONDARY ACCESSION(S): PRJNA408154

REPOSITORIES: GEO

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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

| PRJNA408154 | ENA

ChIP of transcription factor Etv4 (Pea3) Gabpa, Histone deacetylase HDAC2, Ep300 and Histone tails H3K4me1 and H3K27ac in E11.5 limb derived cell line (14Fp cell line)

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Chip-chip from Mouse E11.5 distal limb tissue cells for Gabpa, Ets1, Elf1, Etv4, Etv5 antibody

Project description:Two different groups of Ets transcription factors differentially act directly at the ZRS to define the spatial expression of Shh in the limb. Chromatin immunoprecipitation (ChIP) of Gabpa, Ets1, Etv4, Etv5 and Elf1 and by ChIP-on-chip analysis demonstrated that with the exception of Elf1 all bind directly to the Shh limb enhancer, the ZRS. Array design includes 2 biological replicates for Gabpa and Elf1, and two biological replicates and one dye swap replicate for Ets1, Etv4 and Etv5 samples.

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Single cell RNAseq analysis of undifferentiated skeletal cells in the murine limb bud

Project description:A single cell transcriptional profile of undifferentiated skeletal cells in the murine limb bud marked by Prrx1-cre at E11.5

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ChIP-chip of H3K4me1 and H3K27ac and transcription factors on E11.5 distal limb bud tissue or 14Fp cell line

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Shh and ZRS enhancer co-localization is specific to the zone of polarizing activity

Project description:Limb-specific expression of Shh is regulated by the long-range (~one megabasepair distant) ZRS enhancer. In the mouse, murine limb bud restricted spatiotemporal expression of Shh occurs from ~E10 until E11.5 at the distal posterior margin is essential for the correct formation of the autopod. Here, we have analyzed the higher-order chromatin conformation of Shh in expressing and non-expressing tissues, both by fluorescence in situ hybridization (FISH) and by chromosome conformation capture (5C). Conventional and super-resolution light microscopy identified significantly elevated frequences of Shh/ZRS co-localization only in the Shh expressing regions of the limb bud consistent with the formation of an enhancer-promoter loop. However, Shh-ZRS spatial distances were consistently shorter than intervening distances to a neural enhancer in all tissues and developmental stages analyzed – regardless of Shh expression. 5C also identified a topologically associating domain (TAD) over the Shh-ZRS genomic region and enriched interactions between Shh and ZRS, but in the head, body and limb buds of E11.5 embryos, so also not linked to Shh expression. We show that gene-enhancer (Shh/ZRS) co-localization correlates with the spatiotemporal domain of limb bud-specific Shh expression, but that close Shh/ZRS proximity in the nucleus occurs regardless of whether the gene or enhancer is active. We suggest that this constrained chromatin configuration optimises the opportunity for the active enhancer to locate and instigate Shh expression.

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Bhlha9 deficiency effect in limb bud

Project description:Analysis of mouse limb bud (E10.5) lacking the Bhlha9 gene. Bhlha9 knockout mouse shows syndactyly and poliosis in the limb. This microarray results provides insight into the molecular mechanisms underlying Bhlha9 function in the limb development DNA microarray analysis was performed using Affymetrix mouse genome 430 2.0 array. RNA samples were obtained from the whole limb bud of the E10.5 wild-type and Bhlha9 knockout embryos described above. Total RNA (200 ng) was reverse-transcribed and biotinylated using the GeneChip 3â² IVT Express Kit (Affymetrix). The microarray data were summarized using the MAS 5.0 method.

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Transcription profiling of mouse E10.5 limb bud ZPA and the rest of the E10.5 limb bud from Shhgfpcre heterozygotes separated by FACS

Project description:Comparing gene expression of cells from the E10.5 limb bud ZPA and the rest of the E10.5 limb bud from Shhgfpcre heterozygotes separated by FACS. Experiment Overall Design: 8 samples, 4 ZPA and 4 rest of the limb

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