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E-GEOD-62967 - Constraint and divergence of global gene expression in the mammalian embryo

Status
Released on 14 April 2015, last updated on 19 August 2015
Organism
Mus musculus
Samples (200)
Protocols (2)
Description
We profiled genome-wide gene expression of 170 individual mid-gestation (embryonic day 11.5) whole mouse embryos derived from a 2-generation interspecies mouse cross and asked to what extent genetic variation drives four important parameters of regulatory architecture: allele-specific expression (ASE), imprinting, trans-regulatory effects, and maternal effect. The inbred strain C57BL/6J and wild-derived inbred strain CAST/EiJ were used in reciprocal crosses to generate F1 embryos. F1 progeny were backcrossed to C57BL/6J in reciprocal crosses to generate 154 N2 embryos. We employed a backcross design, in which N2 offspring have genotypically distinct parents, to enable comparison of gene expression for offspring from each side of the reciprocal cross. Our findings demonstrate that genetic variation contributes to widespread gene expression differences during mammalian embryogenesis. Transcriptome analysis of E11.5 mouse embryos: 16 F1 embryos from reciprocally crossed C57BL/6J and CastEi/J parents; and 154 N2 embryos from reciprocal backcross of F1s to the C57BL/6J parent.
Experiment type
RNA-seq of coding RNA 
Contacts
Cheryl L Smith <cheryl.smith@stanford.edu>, Arend Sidow, Jesse M Rodriguez, Julie C Baker, Noah Spies, Serafim Batzoglou
Citation
Constraint and divergence of global gene expression in the mammalian embryo. Spies N, Smith CL, Rodriguez JM, Baker JC, Batzoglou S, Sidow A.
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-62967.idf.txt
Sample and data relationshipE-GEOD-62967.sdrf.txt
Additional data (1)E-GEOD-62967.additional.1.zip
Links