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Platform GPL13346 Query DataSets for GPL13346
Status Public on Mar 31, 2011
Title Agilent custom 2 x 415K human CGH
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Homo sapiens
Manufacturer Agilent Technologies
Manufacture protocol see manufacturer's web site at http://www.agilent.com/
Catalog number Design 023357
 
Description Belfer Institute for Applied Cancer Sciences
Custom 2x415K array for human array-CGH
Arrays of this design have barcodes that begin with 16023357 or 2523357.
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.
Probe coordinates are based on genome build UCSC hg18
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.
 
Contributor(s) Zhang J, Protopopov A, Chin L
Submission date Mar 29, 2011
Last update date Jan 18, 2013
Contact name Alexei Protopopov
Organization name UT MD Anderson Cancer Center
Department IACS
Street address 1901 East Rd
City Houston
State/province TX
ZIP/Postal code 77054
Country USA
 
Samples (21) GSM703398, GSM703399, GSM703400, GSM703401, GSM703402, GSM703403 
Series (1)
GSE28469 Array comparative genomic hybridization (aCGH) study of formalin-fixed paraffin-embedded (FFPE) small gastrointestinal stromal tumors (GISTs) less than 1 cm in greatest diameter (microGISTs)

Data table header descriptions
ID Agilent feature number
ROW RoW
COL Column
SPOT_ID Spot identifier
CONTROL_TYPE Control type
SEQUENCE Probe sequence
GENE_SYMBOL Gene Symbol
GENE_NAME Gene Name
ACCESSION_STRING Accession String
CHROMOSOMAL_LOCATION Chromosomal Location based on hg18
CYTOBAND Cytoband
DESCRIPTION Description
RANGE_GB GenBank accession
RANGE_START
RANGE_END
SPOT_ID

Data table
ID ROW COL SPOT_ID CONTROL_TYPE SEQUENCE GENE_SYMBOL GENE_NAME ACCESSION_STRING CHROMOSOMAL_LOCATION CYTOBAND DESCRIPTION RANGE_GB RANGE_START RANGE_END SPOT_ID
1 796 528 HsCGHBrightCorner pos --HsCGHBrightCorner
2 794 528 DarkCorner pos --DarkCorner
3 792 528 DarkCorner pos --DarkCorner
4 790 528 A_16_P00653900 FALSE CCGATCTGGAACATCTTTATCACTTCATTCATGAACACCTTCATCTCAAGAAAATCTTCT LOC344875 NA 344875|EG|344875 chr3:15181927-15181987 NA Accession id is entrez gene id NC_000003.10 15181927 15181986
5 788 528 A_14_P110624 FALSE ATTTATTTAGTGTCTCAGGAAGGATGATGGGCATATTGCTTGCAAAAGTTGATTTGAATC C9orf66 NA 157983|EG|157983 chr9:204367-204427 NA Accession id is entrez gene id NC_000009.10 204367 204426
6 786 528 A_16_P03598912 FALSE AGAGATGGTGAAGAAGATGGTTTCAAATTTCGACCAGACAACATTTTGGTTTGTGTAAAT CECR1 NA 51816|EG|51816 chr22:16064561-16064621 NA Accession id is entrez gene id NC_000022.9 16064561 16064620
7 784 528 A_16_P00817299 FALSE GAATATCGAACTTCTGTCAACTGTCTCTCACAAATGACCCTCTCTCTTGTGTTTTTATAC EPHB1 NA 2047|EG|2047 chr3:136160997-136161057 NA Accession id is entrez gene id NC_000003.10 136160997 136161056
8 782 528 A_18_P12622581 FALSE AACTAACTAAATTCCTATGAGACTTGCAATGGAACTTCTATGGAACACCTTATACCTGAA SSH2 NA 85464|EG|85464 chr17:25271606-25271666 NA Accession id is entrez gene id NC_000017.9 25271606 25271665
9 780 528 A_16_P02931823 FALSE AAAACGCTTTGCAATGTTGAGACACAGAAAGATTTCGAGAGGCTAATGATGATTGGAA SPTB NA 6710|EG|6710 chr14:64344031-64344089 NA Accession id is entrez gene id NC_000014.7 64344031 64344088
10 778 528 A_16_P20010880 FALSE AGAGCAAGTGACACAGATTCTTCTTTTAAAAGCAGCAAATAAATTTCAAGGAAGTGCACA SLC25A21 NA 89874|EG|89874 chr14:36281599-36281659 NA Accession id is entrez gene id NC_000014.7 36281599 36281658
11 776 528 A_16_P15352591 FALSE ATAGGACATAAACTGACCATCTTTTTCTCCACTTCTACATGAAATAATAAGTGCCTTGGG ASTN NA 460|EG|460 chr1:175135669-175135729 NA Accession id is entrez gene id NC_000001.9 175135669 175135728
12 774 528 A_16_P16246840 FALSE TTTAAACCTGTATTCTCTCCTGAAGAAATACCAGATAGGTAAAATATACTCCCGAGCCAC FHIT NA 2272|EG|2272 chr3:61135960-61136020 NA Accession id is entrez gene id NC_000003.10 61135960 61136019
13 772 528 A_18_P16053429 FALSE ATGGAGACTTGATCTTGCCAACTATCATAATTTTTTGGACATGCAATCCTTACAGTTGAT ELMO1 NA 9844|EG|9844 chr7:37034500-37034560 NA Accession id is entrez gene id NC_000007.12 37034500 37034559
14 770 528 A_16_P17559383 FALSE CAGAGGAACTACAAATAACAAGATTTTTAAAATAATAGATCAGAAGAACGGGAGAAAATA DST NA 667|EG|667 chr6:56768110-56768170 NA Accession id is entrez gene id NC_000006.10 56768110 56768169
15 768 528 A_14_P104190 FALSE CACTAGGAAAAGCCCACATTTTAAAATATGTCAAAATTAGTGAGAAAAAAATCCCACTGG NUDCD2 NA 134492|EG|134492 chr5:162818267-162818327 NA Accession id is entrez gene id NC_000005.8 162818267 162818326
16 766 528 A_16_P02452833 FALSE TGGCCAAATTATACTCAACGATTTAATTAGAAGCACAGATGAAGATACTGGACTTTCAGA NA EG|NA chr11:60137071-60137131 NA Accession id is entrez gene id NC_000011.8 60137071 60137130
17 764 528 A_16_P15597277 FALSE TGGCTATGACCTTTGTTTATTTCAAGAGGGCTAAATTTACTATAAGTGAGCATACCAGGA SPDY1 NA 245711|EG|245711 chr2:28898702-28898762 NA Accession id is entrez gene id NC_000002.10 28898702 28898761
18 762 528 A_16_P20021545 FALSE TGCTGAACTCTTGCTATTAGAGGAAAGGAATGATTAGTTGTTCTCGTTTACAATGTGACA LRFN5 NA 145581|EG|145581 chr14:41301235-41301295 NA Accession id is entrez gene id NC_000014.7 41301235 41301294
19 760 528 A_16_P15178906 FALSE ATCCATTTCCATCTCATGACCTTCTCATTAACTTCAGACTAAGCCATAATAACAGTGCTT NA EG|NA chr1:77467190-77467250 NA Accession id is entrez gene id NC_000001.9 77467190 77467249
20 758 528 A_16_P35102093 FALSE CAGGCATTCAAGAAATATAGAGGCTGAATTACATTTTTTTTGAGGGTCTAAACTTTGCCC NA EG|NA chr1:41499909-41499969 NA Accession id is entrez gene id NC_000001.9 41499909 41499968

Total number of rows: 420288

Table truncated, full table size 84167 Kbytes.




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