FaceBase 24STypes Track Settings
 
FaceBase 24 Sample Types Averaged   (All Expression and Regulation tracks)

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Data coordinates converted via liftOver from: July 2007 (NCBI37/mm9)
Data last updated: 2014-06-02


Note: These data were converted via liftOver from the July 2007 (NCBI37/mm9) version of the track

Description

This dataset represents 24 independent samples of different regions of developing craniofacial structures obtained from embryonic day 8.5, 9.5, 10.5, and 11.5 mouse embryos. RNA was prepared separately from each sample and subjected to a custom mRNA microlabeling protocol so as to allow for hybridization to individual Affymetrix Mouse Genes 1.0 ST Arrays. The various samples correspond to independent replicates from the following cell types:

  • e8.5 Paraxial Mesodem
  • e8.5 Floor Plate Neural Epithelium
  • e8.5 Hindbrain Neural Epithelium
  • e8.5 Non-floor Plate Neural Epithelium
  • e9.5 Olfactory Placode
  • e9.5 Otic Vesicle
  • e9.5 Facial Mesenchyme
  • e9.5 Mandibular Arch
  • e9.5 Maxillary Arch
  • e9.5 Neural Epithelium
  • e10.5 Rathke's Pouch
  • e10.5 Nasal Pit
  • e10.5 Mandibular Arch
  • e10.5 Maxillary Arch
  • e10.5 Mandibular Columnar Epithelium
  • e10.5 Maxillary Columnar Epithelium
  • e10.5 Lateral Nasal Process
  • e10.5 Medial Nasal Process
  • e10.5 Central Neural Epithelium
  • e10.5 Flanking Neural Epithelium
  • e10.5 Lateral Eminence Neural Epithelium
  • e10.5 Medial Eminence Neural Epithelium
  • e11.5 Medial Nasal Prominence

Display Conventions

In dense mode, the track color denotes the average signal over all experiments on a log base 2 scale. Lighter colors correspond to lower signals and darker colors correspond to higher signals. In full mode, the color of each item represents the log base 2 ratio of the signal of that particular experiment to the median signal of all experiments for that probe.

Methods

Microarry data was subjected to RMA normalization and individual gene expression levels per probeset per sample were expressed as a ratio relative to the level of that probeset's expression using whole Postnatal day 1 mouse RNA as a universal reference. Colored blocks extend over the length of the corresponding gene and depict expression in the craniofacial sample relative to that in the reference RNA sample.

Credits

This track was created with the help of the following people:

  • Dissections, RNA purification, and labeling were carried out by Eric Brunskill and Steven Potter.
  • Hybridization and processing by Sean Smith and Hung-Chi Liang in the Cincinnati Children's Hospital gene expression analysis core.
  • Data was analyzed and transformed into UCSC genome browser array format by Andrew Plassard and Bruce Aronow.

This work was part of the Global Gene Expression Atlas of Craniofacial Development project being carried out by the Facebase Consortium.

Contact: Bruce.Aronow@cchmc.org

References

Brunskill EW, Potter AS, Distasio A, Dexheimer P, Plassard A, Aronow BJ, Potter SS. A gene expression atlas of early craniofacial development. Dev Biol. 2014 Jul 15;391(2):133-46. PMID: 24780627