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Platform GPL4089 Query DataSets for GPL4089
Status Public on Aug 14, 2006
Title Agilent-013902 Human Proximal Promoter ChIP-on-Chip Set, Microarray 1 of 2 G4481A
Technology type in situ oligonucleotide
Distribution commercial
Organism Homo sapiens
Manufacturer Agilent Technologies
Manufacture protocol see manufacturer's web site at http://www.agilent.com/
Catalog number G4481A
Support glass
 
Description
The Human Proximal Promoter ChIP-on-chip microarray set contains high-resolution, high performance 60-mer oligonucleotide microarrays that allow the location analysis of DNA binding proteins to promoter regions spanning -0.8KB upstream to +0.2KB downstream of the transcriptional start sites. The two slide set provides coverage for ~17,000 of the best defined human transcripts.

Arrays of this design have barcodes that begin with 16013902 or 2513902.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.
 
Submission date Aug 14, 2006
Last update date Feb 08, 2008
Organization Agilent Technologies
E-mail(s) cag_sales-na@agilent.com
Phone 877-424-4536
URL http://www.agilent.com
Department
Street address
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Samples (22) GSM128952, GSM128979, GSM128986, GSM128987, GSM139286, GSM139289 
Series (5)
GSE5548 Global, comparative analysis of tissue-specific promoter CpG methylation.
GSE5998 Identification of SRF binding sites in Three Human Cell types
GSE8810 methylatedDNA_peripheralBlood

Data table header descriptions
ID Agilent feature number
COL Column
ROW Row
SPOT_ID Spot identifier
CONTROL_TYPE Control type
GB_ACC GenBankAccession
GENE_SYMBOL Gene Symbol
GENE_NAME Gene Name
ACCESSION_STRING Accession String
CHROMOSOMAL_LOCATION Chromosomal Location
CYTOBAND Cytoband
DESCRIPTION Description
GB_RANGE NCBI Build 35.1 Accession.Version[start..end]

Data table
ID COL ROW SPOT_ID CONTROL_TYPE GB_ACC GENE_SYMBOL GENE_NAME ACCESSION_STRING CHROMOSOMAL_LOCATION CYTOBAND DESCRIPTION GB_RANGE
1 103 430 HsCGHBrightCorner pos
2 103 428 NegativeControl neg
3 103 426 A_17_P00011122 FALSE NM_182752 FAM79A ref|NM_182752|ref|FAM79A:-909|ref|NM_017818:25991|mgcs|BC019034:-967|ens|ENST00000334832:40802|ens|ENST00000355885:20247 chr1:003563779-003563828 PROMOTER NC_000001.8[003563779..003563828]
4 103 424 A_17_P00711157 FALSE NM_144977 DENND1B ref|NM_144977|ref|DENND1B:38|mgcs|BC022561:38 chr1:194475919-194475964 INSIDE NC_000001.8[194475919..194475964]
5 103 422 A_17_P00631562 FALSE NM_145034 TOR1AIP2-TOR1AIP1 ref|NM_145034|ref|NM_015602|ref|TOR1AIP2:-4311|ref|TOR1AIP1:-174|mgcs|BC023247:-689|mgcs|BC004969:485|ens|ENST00000305248:-4311 chr1:176582880-176582925 DIVERGENT_PROMOTER NC_000001.8[176582880..176582925]
6 103 420 A_17_P02886476 FALSE NM_000283 PDE6B ref|NM_000283|ref|PDE6B:82|mgcs|BC000249:104 chr4:000609454-000609499 INSIDE NC_000004.9[000609454..000609499]
7 103 418 A_17_P05639559 FALSE NM_015395 DKFZP434B0335 ref|NM_015395|ref|DKFZP434B0335:-553|mgcs|BC053591:-553 chr7:097526645-097526700 PROMOTER NC_000007.11[097526645..097526700]
8 103 416 LACC:GD24C_4_1 pos
9 103 414 A_17_P04666491 FALSE NM_014341 MTCH1 ref|NM_014341|ref|MTCH1:-987|ens|ENST00000358091:-1044 chr6:037062888-037062941 PROMOTER NC_000006.9[037062888..037062941]
10 103 412 A_17_P05174006 FALSE NM_000125 ESR1 ref|NM_000125|ref|ESR1:-731|ens|ENST00000331143:-1093|ens|ENST00000322595:1434 chr6:152220038-152220098 PROMOTER NC_000006.9[152220038..152220098]
11 103 410 A_17_P05455235 FALSE NM_032014 MRPS24 ref|NM_032014|ref|MRPS24:137|mgcs|BC012167:137 chr7:043682178-043682223 INSIDE NC_000007.11[043682178..043682223]
12 103 408 A_17_P04024210 FALSE NM_152408 FLJ35779 ref|NM_152408|ref|FLJ35779:101|mgcs|BC101325:97|ens|ENST00000282199:5157 chr5:075043875-075043935 INSIDE NC_000005.8[075043875..075043935]
13 103 406 A_17_P04689510 FALSE NM_006653 FRS3-C6orf49 ref|NM_006653|ref|NM_013397|ref|FRS3:-1065|ref|C6orf49:-351|mgcs|BC022274:-6727|mgcs|BC010611:-2873|ens|ENST00000335515:14|ccds|CCDS4860.1:-3970 chr6:041856651-041856696 DIVERGENT_PROMOTER NC_000006.9[041856651..041856696]
14 103 404 A_17_P02420635 FALSE NM_176815 DHFRL1 ref|NM_176815|ref|DHFRL1:713|ccds|CCDS2926.1:-592|mgcs|BC045541:713 chr3:095263607-095263667 INSIDE NC_000003.9[095263607..095263667]
15 103 402 A_17_P01897639 FALSE NM_005444 RQCD1 ref|NM_005444|ref|RQCD1:300|mgcs|BC007102:380 chr2:219259459-219259506 INSIDE NC_000002.9[219259459..219259506]
16 103 400 A_17_P00662989 FALSE NM_000963 PTGS2 ref|NM_000963|ref|PTGS2:270|mgcs|BC013734:256 chr1:183380921-183380966 INSIDE NC_000001.8[183380921..183380966]
17 103 398 A_17_P03252500 FALSE NM_198281 LOC285513 ref|NM_198281|ref|LOC285513:-130|ens|ENST00000333209:-130 chr4:090586230-090586275 PROMOTER NC_000004.9[090586230..090586275]
18 103 396 A_17_P00533318 FALSE NM_031282 FCRL4 ref|NM_031282|ref|FCRL4:-414|ens|ENST00000271532:-414 chr1:154381327-154381387 PROMOTER NC_000001.8[154381327..154381387]
19 103 394 A_17_P06078552 FALSE NM_017778 WHSC1L1 ref|NM_017778|ref|WHSC1L1:33639|ref|NM_023034:33639|ens|ENST00000276546:-556 chr8:038325278-038325338 INSIDE NC_000008.9[038325278..038325338]
20 103 392 A_17_P00181552 FALSE NM_003035 SIL ref|NM_003035|ref|SIL:-237|ens|ENST00000243182:-4065|ens|ENST00000337817:-1361|ens|ENST00000360380:-269 chr1:047492050-047492103 PROMOTER NC_000001.8[047492050..047492103]

Total number of rows: 44290

Table truncated, full table size 7665 Kbytes.






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