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Status
Public on Jul 31, 2012
Title
Agilent-024903 Common Primate Array 1x1M (Probe Name version)
Technology type
spotted oligonucleotide
Distribution
custom-commercial
Organism
Homo sapiens
Manufacturer
Agilent Technologies
Manufacture protocol
see manufacturer's web site at http://www.agilent.com/ Agilent's website at: http://www.chem-agilent.com/pdf/G4410-90020v3_1_CGH_ULS_Protocol.pdf
Description
Agilent catalog probes for human (hg18) were downloaded from eArray and aligned against the chimpanzee (panTro2) and rhesus macaque(rheMac2) reference genomes using BLAT. Those probes that had at least 100% match to both reference genomes were similarity filtered based on the human reference genome (i.e. probes with only 1 perfect hit to hg18 were considered for the array). This array should not be considered as a genome-wide, unbiased copy number difference copy number discovery array. Since the probes were required to have 100% identity across human, chimpanzee, and rhesus macaque, the probes cluster together in regions of high conservation. Probe sequences and alignment locations are based on human (hg18),however, great apes and some old world monkeys can also be applied to this array.
Submission date
Nov 26, 2011
Last update date
Nov 27, 2011
Contact name
Charles Lee
E-mail(s)
clee@rics.bwh.harvard.edu
Organization name
Brigham and Women's Hospital/Harvard Medical School
Department
Pathology
Lab
Lee Lab--Molecular Genetic Research Unit
Street address
221 Longwood Ave., EBRC-422
City
Boston
State/province
MA
ZIP/Postal code
02115
Country
USA
Samples (17)
GSM839690 , GSM839691 , GSM839692 , GSM839693 , GSM839694 , GSM839695
GSM839696 ,
GSM839697 ,
GSM839698 ,
GSM839699 ,
GSM839700 ,
GSM839701 ,
GSM839702 ,
GSM839703 ,
GSM839704 ,
GSM839705 ,
GSM839706
Series (1)
GSE33960
Regulatory element copy number differences shape primate expression profiles
Data table header descriptions
ID
Agilent probe name
SystematicName
Chromosome
Chromosomal location
RANGE_GB
Start
Stop
SEQUENCE
Data table
ID
SystematicName
Chromosome
RANGE_GB
Start
Stop
SEQUENCE
A_14_P100044
chr14:23804584-23804635
chr14
NC_000014.7
23804584
23804635
TTGGTAGCCTGAGAGGGCCTCTCCATTCTTTATTCAGTCCCAATAAGTTAAA
A_14_P100049
chr3:188922846-188922905
chr3
NC_000003.10
188922846
188922905
ACTACATCATGGGATGAACATTGTAAAGTGTTACAGTATCCTTTGGGTAGATTCTGAGAA
A_14_P100053
chr3:45748565-45748624
chr3
NC_000003.10
45748565
45748624
TTCCATAAGGAATGTAAAAATATGAGATGGGATCGACTAAGTATTTTATTGGATCAGGTA
A_14_P100071
chr16:65784870-65784915
chr16
NC_000016.8
65784870
65784915
TCACACTTTGGCCTACGTCACTCATGAGGACATCTGCAGATGCTTT
A_14_P100072
chr8:109567976-109568035
chr8
NC_000008.9
109567976
109568035
GGAAACATTGCAGATCACCCAGTCTTAAGGTTTCAAAAACTCTTTGACATTAGATTTCAC
A_14_P100074
chr12:91782828-91782887
chr12
NC_000012.10
91782828
91782887
CTTCATAATGTTTGAAAAGTTCATCAGCAGATCCAAGAGATTTCATACACTGGGGACATA
A_14_P100087
chr9:73530320-73530379
chr9
NC_000009.10
73530320
73530379
AAAATTTGAATGGACCCTGTTGTTATAAAATATACCCAATGGAGTGAGTTCTGGTTTTGC
A_14_P100092
chr19:10302121-10302170
chr19
NC_000019.8
10302121
10302170
CATGGCCCCACAAACCTGTCCCTTTGTATTTGTCCACAAAACAGTATTTG
A_14_P100100
chr14:23082779-23082838
chr14
NC_000014.7
23082779
23082838
ACCCATTTGTGACAACATCTCTTAAAGTTGAAGGTCTACACATGTGTATCCATATTAGCA
A_14_P100129
chrX:14502356-14502415
chrX
NC_000023.9
14502356
14502415
ATTCTCATTGCATTCTGCAGGTCCTCCAGTAAACGTTACTTGCAATATTTTTATCAACAG
A_14_P100131
chr5:176595458-176595517
chr5
NC_000005.8
176595458
176595517
AGCCAAGCAAGTGGCTTTTGGAATATACAGAAGAATATGATCAGATATTTGCTCCTAAGA
A_14_P100141
chr3:66512060-66512119
chr3
NC_000003.10
66512060
66512119
GCCTCTCAGAAGCAGCAAATTCACATATTTTGTGGAAGTAAGATTAGTCAGTTAACTGTC
A_14_P100155
chr6:31786112-31786162
chr6
NC_000006.10
31786112
31786162
CTCGATTCCTCAGTTCAAACCCGAAATCCAGGTCTATGAGAACATCCATTT
A_14_P100173
chr6:35824273-35824322
chr6
NC_000006.10
35824273
35824322
TTTCTCTATTCCCATCACAGGTTCACTCCAACTTCCTAAACCTGTTCCAG
A_14_P100181
chr3:142177906-142177960
chr3
NC_000003.10
142177906
142177960
CTCATCTAGTGAGACAGATTCCAAACACAGCCATTATGATGGCCACCTATGAATT
A_14_P100194
chr14:102036198-102036257
chr14
NC_000014.7
102036198
102036257
ACAGTTTTCTTTCTGGTTTTAATTTTTAGTTGTGCTTTGAGTCAGTGCAATAAACTAGAC
A_14_P100212
chr4:78745926-78745975
chr4
NC_000004.10
78745926
78745975
CTACTGGAGACAAAGGCAGTGGGAGGGCCCTTACTGGTATAAATAAATAG
A_14_P100226
chr7:31087833-31087892
chr7
NC_000007.12
31087833
31087892
CCTATGTCTGTATTTTTCAGGAGAGTCTGATTTTGGTGACAGTAACTCCTTAGATCTCTC
A_14_P100262
chr13:36390522-36390581
chr13
NC_000013.9
36390522
36390581
CTCTGACAAAGATAACCAGTCAAGCATAAAAATGGGAGTTGGTTGTGTCAGAATACATTA
A_14_P100278
chr2:153324487-153324546
chr2
NC_000002.10
153324487
153324546
GTGTTTTTCTTTTTTTCTAGGAAACTGACTGGACATTCTTTCCACATGGGCTATAGCATG
Total number of rows: 963331 Table truncated, full table size 123233 Kbytes .
Supplementary data files not provided