Schema for Sestan Brain - Sestan Lab Human Brain Atlas Microarrays
  Database: hg19    Primary Table: sestanBrainAtlas    Row Count: 877,469   Data last updated: 2010-08-06
Format description: Browser extensible data with 15 fields including experiment values
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 17120int(10) unsigned Start position in chromosome
chromEnd 17183int(10) unsigned End position in chromosome
name 2390568varchar(255) Name of item
score 0int(10) unsigned Score from 0-1000
strand -char(1) + or -
thickStart 17120int(10) unsigned Start of where display should be thick (start codon)
thickEnd 17183int(10) unsigned End of where display should be thick (stop codon)
reserved 0int(10) unsigned Used as itemRgb as of 2004-11-22
blockCount 1int(10) unsigned Number of blocks
blockSizes 63longblob Comma separated list of block sizes
chromStarts 0,longblob Start positions relative to chromStart
expCount 95int(10) unsigned 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 0.418087,0.0955225,-0.47721...longblob Comma separated list of experiment scores

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsexpCountexpIdsexpScores
585chr1171201718323905680-171201718301630,950,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.418087,0.0955225,-0.477212,0.048923,-0.11261,-0.00196759,-0.776883,-0.314675,-0.195021,-0.743863,-0.295264,0.246773,1.24955,0. ...
585chr1177731791023905740-1777317910011370,950,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.690635,0.486202,0.423499,0.884233,0.404309,0.331875,1.22238,0.301079,-1.20858,-0.590146,0.877455,0.446346,1.09318,1.03443,0.27 ...
585chr1202382056923905830-2023820569013310,950,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.46975,-0.0634109,-0.764968,-0.134139,-0.582812,0.12378,-0.411052,-0.24772,-0.231436,-0.0418302,0.00751018,-0.466981,-0.133858, ...
585chr1529375306823151310+5293753068011310,950,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.15461,0.153974,0.0585965,0.152897,0.289199,0.0544073,0.0269655,0.0782757,0.170236,0.0551895,0.0102747,-0.00221387,0.307787,0.0 ...
585chr1636556369723151330+636556369701420,950,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...-0.480028,-1.40917,1.02369,0.124988,-0.790176,-0.614593,0.80978,0.259849,-0.632662,-0.630657,-0.314529,1.06793,-1.05945,-0.49194 ...
585chr1655356556223151270+655356556201270,950,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.199905,0.0705677,0.0714879,-0.0983097,1.0886,0.0768147,-0.157092,0.714312,-0.0502537,0.0415264,0.0293931,0.144555,1.02098,0.37 ...
585chr1723047232923906080-723047232901250,950,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...-0.744522,-0.444655,-0.660479,1.05819,-0.35042,-0.643859,-0.168487,-0.146599,-0.0573659,-0.0717206,-0.726033,-0.933364,-0.252574 ...
585chr1960169663723906410-9601696637016210,950,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...-1.12888,0.0686169,0.252342,1.2987,0.438521,0.0983189,0.00691155,-0.376695,0.423217,0.206014,0.346476,0.798898,0.855954,-0.50327 ...
585chr1987189898223906430-9871898982012640,950,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.0790222,-0.0536098,-0.274069,-0.00633079,0.267683,0.26805,0.28586,0.629358,0.0556511,0.00499217,-0.456561,-0.150463,0.397546,0 ...
585chr111584711599123151460+115847115991011440,950,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.00248418,-0.493508,0.902987,1.21268,0.802198,-1.2349,-1.32232,-1.4095,0.636576,0.352459,0.369951,0.482456,0.256,-0.476361,-0.3 ...

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

Sestan Brain (sestanBrainAtlas) Track Description
 

Description

This track displays exon microarray expression data from the late mid-fetal human brain, generated by the Sestan Lab at Yale University. The data represent 13 brain regions, including nine areas of neocortex, and both hemispheres. By default, arrays are grouped by the median for each brain region, including each neocortical area. Alternatively, neocortex areas can be grouped together; arrays can be grouped by mean; or all 95 arrays can be shown individually.

Methods

RNA was isolated from 13 brain regions, from both hemispheres, of four late mid-fetal human brains, with a total PMI of less than one hour, and hybridized to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into Partek GS using Robust Multichip Average (RMA) background correction, quantile normalization, and GC content correction. The normalized data were then converted to log-ratios, relative to arrays hybridized with RNA pooled from all regions of the same brain. Signal log-ratios are displayed here as green for negative (underexpression) and red for positive (overexpression).

The probe set for this microarray track can be displayed by turning on the Affy HuEx 1.0 track. Core, extended, and full probe sets are shown. "Bounded" probe sets - exons that lie within the intron of more than one gene - and potentially cross-hybridizing probe sets were filtered from this dataset, leaving ~875K probe sets.

Credits

The data for this track were generated and analyzed by Matthew B. Johnson, Yuka Imamura Kawasawa, Christopher Mason, and the Yale Neuroscience Microarray Center.

Links

The raw microarray data are available via the NCBI Gene Expression Omnibus.

More information is available at https://hbatlas.org/.