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This text describes the data presented in the paper: "Msx1 haploinsufficiency modifies the Pax9-deficient cardiovascular phenotype" by Khasawneh et al.

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Introductory information
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Files included in the data deposit (include a short description of what data are contained): 

1) Magnetic Resonance Imaging datasets of images shown in Figures 1, 4 and Additional File 2. Data are AmiraMesh (.am) files of each embryo shown in the figures.
2) microCT imaging datasets of images shown in Figure 2. Data are AmiraMesh (.am) files of each embryo shown in the figures.
3) High Resolution Episcopic Microscopy imaging datasets of images shown in Additional File 2. Data are AmiraMesh (.am) files of each embryo shown in the figures.


Explain the relationship between multiple data sets, if required:

Different methods were employed depending on the number and stage of embryos needing to be imaged for analysis.
MRI was used for the simultaneous imaging of 32 embryos at E15.5.
microCT was used for imaging up to four E12.5 or E15.5 embryos at a time.
HREM was used for earlier stage embryos (E12.5 and E10.5).


Key words used to describe the data:

MRI, uCT, HREM, cardiovascular anatomy



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Methodological information
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A brief method description of what the data is, how and why it was collected or created, and how it was processed:

Methodology for each imaging type has been published:

Degenhardt K, Wright AC, Horng D, Padmanabhan A, Epstein JA: Rapid 3D phenotyping of cardiovascular development in mouse embryos by micro-CT with iodine staining. Circ Cardiovasc Imaging 2010, 3(3):314-322.

Bamforth SD, Schneider JE, Bhattacharya S: High-throughput analysis of mouse embryos by magnetic resonance imaging. Cold Spring Harb Protoc 2012, 2012(1):93-101.

Weninger WJ, Geyer SH, Martineau A, Galli A, Adams DJ, Wilson R, Mohun TJ: Phenotyping structural abnormalities in mouse embryos using high-resolution episcopic microscopy. Dis Model Mech 2014, 7(10):1143-1152.


Imaging data was acquired to facilitate the accurate identification	of cardiovascular abnormalities. Each methodology generates a stack of TIFF or JPEG images that are imported into Amira Imaging software, creating an AmiraMesh (.am) file of the embryo that can be examined in any orientation. 3D images were created to show the defects in the paper.

*Note* Embryo SID1904 shown in Additional File 2, panel J, is a control embryo (E10.5) analysed from HREM data available at https://dmdd.org.uk/details/DMDD1904.

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Contact
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Please contact rdm@ncl.ac.uk for further information