NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL14930 Query DataSets for GPL14930
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 
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.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap