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SRX2320874: GSM2371693: RNAseq_E11.5-PA2_1; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 73.9M spots, 3.7G bases, 1.6Gb downloads

Submitted by: NCBI (GEO)
Study: Gene bivalency at Polycomb domains regulates cranial neural crest positional identity [RNA-seq]
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The cranial neural crest cells are pluripotent cells that provide head skeletogenic mesenchyme and are crucial for craniofacial patterning. Here, we analyzed the in vivo chromatin landscapes of mouse cranial neural crest subpopulations. Early postmigratory neural crest subpopulations contributing to distinct mouse craniofacial structures displayed similar chromatin accessibility patterns, yet differed transcriptionally. Accessible promoters and enhancers of differentially silenced genes carried H3K27me3/H3K4me2 bivalent chromatin marks embedded in large Ezh2-dependent Polycomb domains, indicating transcriptional poising. These postmigratory bivalent regions were already present in neural crest premigratory progenitors. At Polycomb domains, H3K27me3 antagonized H3K4me2 deposition, which was restricted to accessible sites. Thus, bivalent Polycomb domains provide a chromatin template for the regulation of cranial neural crest cell positional identity in vivo contributing novel insights into the epigenetic regulation of face morphogenesis. Overall design: RNAseq, ChIPseq (single H3K27me3, H3K4me2 and H3K27ac ChIPseq; sequential H3K27me3/H3K4me2 ChIPseq) and ATACseq profiling of cranial neural crest cell (NCC) progenitors (E8.5) and postmigratory subpopulations (FNP, Mx, Md, PA2; E10.5 and E11.5) of wildtype, Ezh2-conditional knockout, Hoxa2-temporal knockout and Hoxa2-overexpression genotypes.
Sample: RNAseq_E11.5-PA2_1
SAMN05968081 • SRS1777131 • All experiments • All runs
Organism: Mus musculus
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Selection: cDNA
Layout: SINGLE
Construction protocol: Embryonic tissues were micro-dissected at E8.5, E10.5 or E11.5 and incubated in trypsin 0.5%/EDTA 1X at 37 °C for 10 minutes and rinsed in DMEM 1X/ FBS 10%. Cranial neural crest cells (CNCCs) were then dissociated with a pipette, filtered and collected by FACS. After sorting, CNCCs were pelleted by centrifugation for 5 minutes, 1000 rpm at 4°C. Total RNA was extracted using PicoPure® Kit (KIT0204 Life Technologies). For sequencing of total RNA, unstranded RNA-Seq libraries were prepared using the ScriptSeq v2 RNA-Seq Library preparation Kit. Three samples with different barcodes were mixed at equimolar ratios per pool. Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single-end reads) according to Illumina standards.
Runs: 1 run, 73.9M spots, 3.7G bases, 1.6Gb
Run# of Spots# of BasesSizePublished


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