Schema for Allen Brain - Allen Brain Atlas Probes
  Database: hg19    Primary Table: allenBrainAli    Row Count: 17,995   Data last updated: 2009-09-30
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 716int(10) unsigned range Number of bases that match that aren't repeats
misMatches 161int(10) unsigned range Number of bases that don't match
repMatches 30int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName RP_040604_01_H04varchar(255) values Query sequence name
qSize 929int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 929int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 249250621int(10) unsigned range Target sequence size
tStart 15011int(10) unsigned range Alignment start position in target
tEnd 18005int(10) unsigned range Alignment end position in target
blockCount 13int(10) unsigned range Number of blocks in alignment
blockSizes 27,110,48,64,6,42,28,19,202...longblob   Size of each block
qStarts 0,27,138,186,251,262,313,34...longblob   Start of each block in query.
tStarts 15011,15795,15905,16606,166...longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg19.allenBrainUrl.name (via allenBrainAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5857161613000000-RP_040604_01_H049290929chr124925062115011180051327,110,48,64,6,42,28,19,202,60,73,137,91,0,27,138,186,251,262,313,347,366,568,628,701,838,15011,15795,15905,16606,16670,16676,16718,16746,16853,17232,17295,17605,17914,
591215123000000-RP_051212_02_G094250402chr12492506218686178690651726,37,8,3,14,6,10,46,54,31,9,21,21,12,9,14,17,23,50,87,95,98,112,119,129,237,291,322,331,352,373,385,394,408,868617,868643,868681,868691,868701,868716,868722,868736,868853,868913,868950,868961,868986,869008,869021,869031,869048,
591781132000000+RP_050503_03_F119130913chr1249250621897773899873778,214,145,168,89,74,145,0,78,292,437,605,694,768,897773,898083,898488,898716,899299,899486,899728,
591545222000000-RP_050324_03_F118100810chr12492506219113829146672117,10,11,7,57,51,38,70,126,39,37,17,9,9,15,61,9,33,90,21,40,0,18,29,41,49,106,157,210,280,406,451,488,505,514,523,538,599,611,650,740,770,911382,911399,911409,911420,911427,911489,911541,911579,911878,914260,914299,914348,914366,914377,914389,914407,914471,914480,91 ...
59219275000000-RP_050421_02_B127940303chr12492506219346269349601322,24,49,6,33,9,12,24,10,22,14,25,17,491,520,544,594,600,644,668,680,704,714,736,750,777,934626,934648,934711,934760,934768,934801,934810,934824,934858,934870,934901,934918,934943,
592410136000000+RP_050125_01_B055460546chr12492506219488719498571012,8,15,13,16,134,9,323,13,3,0,12,20,35,48,64,198,207,530,543,948871,948884,948895,948926,948940,949363,949500,949512,949837,949854,
592451157000000+RP_050419_04_D056450645chr12492506219898979907831334,173,128,31,6,49,17,18,4,92,16,8,32,0,34,211,342,375,381,430,449,474,494,586,605,613,989897,990203,990376,990504,990535,990542,990592,990609,990627,990631,990724,990740,990751,
5925071663600000-RP_050713_04_F067190719chr1249250621100733010094917107,41,477,21,31,28,4,0,113,157,634,656,687,715,1007330,1007437,1007478,1009395,1009416,1009448,1009487,
59215883000000-RP_050927_01_G098110259chr1249250621101760610179101631,14,36,17,11,12,8,15,10,4,7,19,5,9,30,13,552,592,606,642,666,677,689,697,714,724,728,735,754,759,768,798,1017606,1017640,1017655,1017697,1017714,1017727,1017741,1017750,1017765,1017777,1017793,1017810,1017835,1017845,1017866,1017897,
593545106000000+RP_051005_03_E066840654chr1249250621111931511329607156,7,134,117,94,98,45,0,156,163,297,414,508,609,1119315,1120240,1120355,1131979,1132472,1132817,1132915,

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

Allen Brain (allenBrainAli) Track Description
 

Description

This track provides a link into the Allen Brain Atlas (ABA) images for this probe. The ABA is an extensive database of high resolution in-situ hybridization images of adult male mouse brains covering the majority of genes.

Methods

The ABA created a platform for high-throughput in situ hybridization (ISH) that allows a highly systematic approach to analyzing gene expression in the brain. ISH is a technique that allows the cellular localization of mRNA transcripts for specific genes. Labeled antisense probes, specific to a particular gene, are hybridized to cellular (sense) transcripts and subsequent detection of the bound probe produces specific labeling in those cells expressing the particular gene. This method involves tagged nucleotides detected by colorimetric methods.

The platform used for the ABA utilizes this non-isotopic approach, with digoxigenin-labeled nucleotides incorporated into a riboprobe produced by in vitro transcription. This method produces a label that fills the cell body, in contrast to autoradiography that produces scattered silver grains surrounding each labeled cell. To enhance the ability to detect low level expression, the ABA has incorporated a tyramide signal amplification step into the protocol that greatly increases sensitivity. The specific methodology is described in detail within the ABA Data Production Processes document.

Credits

Thanks to the Allen Institute for Brain Science in general, and Susan Sunkin in particular, for coordinating with UCSC on this annotation.