Schema for FaceBase 24STypes - FaceBase 24 Sample Types Averaged
  Database: mm9    Primary Table: FaceBase24SampleTypesAvg    Row Count: 18,986   Data last updated: 2014-05-22
Format description: Browser extensible data with 15 fields including experiment values
fieldexampleSQL type info description
bin 608smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 3044314int(10) unsigned range Start position in chromosome
chromEnd 3044814int(10) unsigned range End position in chromosome
name 10353307varchar(255) values Name of item
score 1000int(10) unsigned range Score from 0-1000
strand +char(1) values + or -
thickStart 3044314int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 3044814int(10) unsigned range End of where display should be thick (stop codon)
reserved 0int(10) unsigned range Used as itemRgb as of 2004-11-22
blockCount 1int(10) unsigned range Number of blocks
blockSizes 500,longblob   Comma separated list of block sizes
chromStarts 0,longblob   Start positions relative to chromStart
expCount 24int(10) unsigned range Number of experiment values
expIds 0,1,2,3,4,5,6,7,8,9,10,11,1...longblob   Comma separated list of experiment IDs
expScores -0.011642,-0.003290,0.06248...longblob   Comma separated list of experiment scores

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsexpCountexpIdsexpScores
608chr130443143044814103533071000+3044314304481401500,0,240,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,-0.011642,-0.003290,0.062482,-0.021241,0.176800,0.416812,0.309314,0.093580,-0.131254,0.008840,0.003138,0.808387,0.200252,0.38180 ...
608chr130443143044814103446141000+3044314304481401500,0,240,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,0.016432,-0.055906,0.038505,-0.050273,0.104530,0.284629,0.093693,0.023573,-0.089599,-0.044785,-0.014574,0.406987,0.125514,0.1751 ...
608chr130443143044814104999671000+3044314304481401500,0,240,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,-0.019049,-0.038196,-0.019084,0.026602,0.034294,0.195514,0.033795,-0.022070,-0.056094,-0.016230,-0.047192,-0.036543,-0.021414,-0 ...
76chr131959823661579103529201000-3195982366157901465597,0,240,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,0.129511,-0.118182,-0.067053,-0.259610,-0.111871,0.285464,0.125147,0.114368,-0.203459,-0.134838,-0.150595,0.390076,0.309470,0.33 ...
613chr137738183773879105831971000-377381837738790161,0,240,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,2.371190,0.336166,0.024412,0.944622,0.238684,0.687329,-0.021581,-0.077018,0.152390,0.037577,0.752747,0.784817,0.281839,0.026982, ...
619chr144810094486494103529361000-44810094486494015485,0,240,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,-0.195305,0.580197,-0.193088,-0.276838,-0.153192,-0.069477,-0.009792,0.239377,0.355838,0.384368,-0.243996,0.012726,-0.099761,0.7 ...
621chr147632874775820103529471000-476328747758200112533,0,240,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,-0.222501,0.358988,0.062837,0.370665,0.372216,-1.048460,-0.305197,0.141254,0.225821,0.073452,0.024547,-2.256710,-0.821281,-0.886 ...
77chr147978694876851103446241000+479786948768510178982,0,240,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,0.056925,1.707340,1.605460,2.749630,2.014930,0.170084,-0.211885,-0.203799,1.645000,1.163120,0.484629,-1.194520,-0.724309,-1.4993 ...
77chr148477754887987103446331000+484777548879870140212,0,240,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,-0.397147,-0.137525,-0.327160,0.572742,-0.107352,0.221588,-0.379833,0.053690,0.369125,-0.004428,0.347101,-0.988072,0.168374,0.19 ...
77chr148477754887987104263011000+484777548879870140212,0,240,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,-1.626810,0.484928,0.156351,0.896072,0.406947,-0.697719,-1.131880,-0.706531,0.388521,0.364097,-0.325089,-2.105210,-2.436290,-1.7 ...

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

FaceBase 24STypes (FaceBase24SampleTypesAvg) Track Description
 

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