Database: hg19    Primary Table: allenBrainAli    Row Count: 17,995
Format description: Summary info about a patSpace alignment

field	example	SQL type	info	description
bin	585	smallint(5) unsigned	range	Indexing field to speed chromosome range queries.
matches	716	int(10) unsigned	range	Number of bases that match that aren't repeats
misMatches	161	int(10) unsigned	range	Number of bases that don't match
repMatches	30	int(10) unsigned	range	Number of bases that match but are part of repeats
nCount	0	int(10) unsigned	range	Number of 'N' bases
qNumInsert	0	int(10) unsigned	range	Number of inserts in query
qBaseInsert	0	int(10) unsigned	range	Number of bases inserted in query
tNumInsert	0	int(10) unsigned	range	Number of inserts in target
tBaseInsert	0	int(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_H04	varchar(255)	values	Query sequence name
qSize	929	int(10) unsigned	range	Query sequence size
qStart	0	int(10) unsigned	range	Alignment start position in query
qEnd	929	int(10) unsigned	range	Alignment end position in query
tName	chr1	varchar(255)	values	Target sequence name
tSize	249250621	int(10) unsigned	range	Target sequence size
tStart	15011	int(10) unsigned	range	Alignment start position in target
tEnd	18005	int(10) unsigned	range	Alignment end position in target
blockCount	13	int(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.

      hg19.allenBrainUrl.name (via allenBrainAli.qName)

bin	matches	misMatches	repMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	716	161	30	0	0	0	0	0	-	RP_040604_01_H04	929	0	929	chr1	249250621	15011	18005	13	27,110,48,64,6,42,28,19,202,60,73,137,91,	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,
591	215	123	0	0	0	0	0	0	-	RP_051212_02_G09	425	0	402	chr1	249250621	868617	869065	17	26,37,8,3,14,6,10,46,54,31,9,21,21,12,9,14,17,	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,
591	781	132	0	0	0	0	0	0	+	RP_050503_03_F11	913	0	913	chr1	249250621	897773	899873	7	78,214,145,168,89,74,145,	0,78,292,437,605,694,768,	897773,898083,898488,898716,899299,899486,899728,
591	545	222	0	0	0	0	0	0	-	RP_050324_03_F11	810	0	810	chr1	249250621	911382	914667	21	17,10,11,7,57,51,38,70,126,39,37,17,9,9,15,61,9,33,90,21,40,	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 ...
592	192	75	0	0	0	0	0	0	-	RP_050421_02_B12	794	0	303	chr1	249250621	934626	934960	13	22,24,49,6,33,9,12,24,10,22,14,25,17,	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,
592	410	136	0	0	0	0	0	0	+	RP_050125_01_B05	546	0	546	chr1	249250621	948871	949857	10	12,8,15,13,16,134,9,323,13,3,	0,12,20,35,48,64,198,207,530,543,	948871,948884,948895,948926,948940,949363,949500,949512,949837,949854,
592	451	157	0	0	0	0	0	0	+	RP_050419_04_D05	645	0	645	chr1	249250621	989897	990783	13	34,173,128,31,6,49,17,18,4,92,16,8,32,	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,
592	507	166	36	0	0	0	0	0	-	RP_050713_04_F06	719	0	719	chr1	249250621	1007330	1009491	7	107,41,477,21,31,28,4,	0,113,157,634,656,687,715,	1007330,1007437,1007478,1009395,1009416,1009448,1009487,
592	158	83	0	0	0	0	0	0	-	RP_050927_01_G09	811	0	259	chr1	249250621	1017606	1017910	16	31,14,36,17,11,12,8,15,10,4,7,19,5,9,30,13,	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,
593	545	106	0	0	0	0	0	0	+	RP_051005_03_E06	684	0	654	chr1	249250621	1119315	1132960	7	156,7,134,117,94,98,45,	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.

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.