Schema for FaceBase 24STypes - FaceBase 24 Sample Types Averaged |
|---|
| |
Database: mm10 Primary Table: FaceBase24SampleTypesAvg Row Count: 18,956 Data last updated: 2014-06-02
Format description: Browser extensible data with 15 fields including experiment values
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
|---|
| bin | 608 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
| chromStart | 3054233 | int(10) unsigned | range | Start position in chromosome |
| chromEnd | 3054733 | int(10) unsigned | range | End position in chromosome |
| name | 10353307 | varchar(255) | values | Name of item |
| score | 1000 | int(10) unsigned | range | Score from 0-1000 |
| strand | + | char(1) | values | + or - |
| thickStart | 3054233 | int(10) unsigned | range | Start of where display should be thick (start codon) |
| thickEnd | 3054733 | int(10) unsigned | range | End of where display should be thick (stop codon) |
| reserved | 0 | int(10) unsigned | range | Used as itemRgb as of 2004-11-22 |
| blockCount | 1 | int(10) unsigned | range | Number of blocks |
| blockSizes | 500, | longblob | | Comma separated list of block sizes |
| chromStarts | 0, | longblob | | Start positions relative to chromStart |
| expCount | 24 | int(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,-0.00329,0.062482... | longblob | | Comma separated list of experiment scores |
|
| |
|
|
|
Sample Rows
|
|---|
| |
| bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | expCount | expIds | expScores |
|---|
| 608 | chr1 | 3054233 | 3054733 | 10353307 | 1000 | + | 3054233 | 3054733 | 0 | 1 | 500, | 0, | 24 | 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23, | -0.011642,-0.00329,0.062482,-0.021241,0.1768,0.416812,0.309314,0.09358,-0.131254,0.00884,0.003138,0.808387,0.200252,0.381808,0.6 ... |
| 608 | chr1 | 3054233 | 3054733 | 10344614 | 1000 | + | 3054233 | 3054733 | 0 | 1 | 500, | 0, | 24 | 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23, | 0.016432,-0.055906,0.038505,-0.050273,0.10453,0.284629,0.093693,0.023573,-0.089599,-0.044785,-0.014574,0.406987,0.125514,0.17518 ... |
| 608 | chr1 | 3054233 | 3054733 | 10499967 | 1000 | + | 3054233 | 3054733 | 0 | 1 | 500, | 0, | 24 | 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23, | -0.019049,-0.038196,-0.019084,0.026602,0.034294,0.195514,0.033795,-0.02207,-0.056094,-0.01623,-0.047192,-0.036543,-0.021414,-0.0 ... |
| 76 | chr1 | 3205901 | 3671498 | 10352920 | 1000 | - | 3205901 | 3671498 | 0 | 1 | 465597, | 0, | 24 | 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23, | 0.129511,-0.118182,-0.067053,-0.25961,-0.111871,0.285464,0.125147,0.114368,-0.203459,-0.134838,-0.150595,0.390076,0.30947,0.3313 ... |
| 613 | chr1 | 3783737 | 3783798 | 10583197 | 1000 | - | 3783737 | 3783798 | 0 | 1 | 61, | 0, | 24 | 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23, | 2.37119,0.336166,0.024412,0.944622,0.238684,0.687329,-0.021581,-0.077018,0.15239,0.037577,0.752747,0.784817,0.281839,0.026982,0. ... |
| 619 | chr1 | 4490928 | 4496413 | 10352936 | 1000 | - | 4490928 | 4496413 | 0 | 1 | 5485, | 0, | 24 | 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23, | -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 ... |
| 621 | chr1 | 4773206 | 4785739 | 10352947 | 1000 | - | 4773206 | 4785739 | 0 | 1 | 12533, | 0, | 24 | 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23, | -0.222501,0.358988,0.062837,0.370665,0.372216,-1.04846,-0.305197,0.141254,0.225821,0.073452,0.024547,-2.25671,-0.821281,-0.88668 ... |
| 77 | chr1 | 4807788 | 4886770 | 10344624 | 1000 | + | 4807788 | 4886770 | 0 | 1 | 78982, | 0, | 24 | 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23, | 0.056925,1.70734,1.60546,2.74963,2.01493,0.170084,-0.211885,-0.203799,1.645,1.16312,0.484629,-1.19452,-0.724309,-1.49937,-1.5016 ... |
| 622 | chr1 | 4857694 | 4897906 | 10344633 | 1000 | + | 4857694 | 4897906 | 0 | 1 | 40212, | 0, | 24 | 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23, | -0.397147,-0.137525,-0.32716,0.572742,-0.107352,0.221588,-0.379833,0.05369,0.369125,-0.004428,0.347101,-0.988072,0.168374,0.1975 ... |
| 622 | chr1 | 4857694 | 4897906 | 10426301 | 1000 | + | 4857694 | 4897906 | 0 | 1 | 40212, | 0, | 24 | 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23, | -1.62681,0.484928,0.156351,0.896072,0.406947,-0.697719,-1.13188,-0.706531,0.388521,0.364097,-0.325089,-2.10521,-2.43629,-1.72976 ... |
|
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
| |
|
|
|
US Server