Transcriptomics

Dataset Information

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A 3D molecular atlas of the chick embryonic heart


ABSTRACT: We performed a detailed analysis of gene expression in the 2-day (HH12) embryonic chick heart. RNA-seq of 13 microdissected heart regions reveals regionalised expression of about 15,000 genes (Dataset 1). Of these, 131 genes that are differentially expressed (FPKM ≥20, fold change ≥1.1-4.0) within a region compared to the other 12 regions were studied by in situ hybridisation (bold text in Dataset 1) and used to generate a 3D molecular map of the heart at this stage of development.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Gallus gallus  

SUBMITTER: Claudio Stern  

PROVIDER: E-MTAB-7663 | ArrayExpress | 2019-10-02

SECONDARY ACCESSION(S): ERP113721

REPOSITORIES: ArrayExpress, ENA

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Publications

A 3D molecular atlas of the chick embryonic heart.

Anderson Claire C   Hill Bill B   Lu Hui-Chun HC   Moverley Adam A   Yang Youwen Y   Oliveira Nidia M M NMM   Baldock Richard A RA   Stern Claudio D CD  

Developmental biology 20190705 1


We present a detailed analysis of gene expression in the 2-day (HH12) embryonic chick heart. RNA-seq of 13 micro-dissected regions reveals regionalised expression of 15,570 genes. Of these, 132 were studied by in situ hybridisation and a subset (38 genes) was mapped by Optical Projection Tomography or serial sectioning to build a detailed 3-dimensional atlas of expression. We display this with a novel interactive 3-D viewer and as stacks of sections, revealing the boundaries of expression domain  ...[more]

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