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Platform GPL6852 Query DataSets for GPL6852
Status Public on Aug 30, 2008
Title UMDNJ/Lukac Human herpesvirus 8/107+GAPDH
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Human gammaherpesvirus 8
Manufacturer Lukac laboratory and Center for Applied Genomics/UMDNJ/NJ Medical School
Manufacture protocol The KSHV microarray consists of 60-70-mer oligonucleotides (oligos) designed to detect 96 predicted KSHV ORFs and splice variants, identical to those published by Lu, et al (Journal of Virology, December 2004, p. 13637-13652, Vol. 78, No. 24), updated to include newer annotated transcripts. A detector oligo for the Human housekeeping genes glyceraldehyde-3-phosphate dehydrogenase was also synthesized. Operon Biotechnologies synthesized all oligos with 5' amino-C6 modifications. Oligos were spotted in triplicate onto poly-L-lysine-coated glass microscope slides using a GeneMachines Omnigrid 100 Arrayer (Genomic Solutions) and SMP3 pins (Telechem).
Support glass
Coating polysine
 
 
Contributor(s) Bu W, Palmeri D, Aris V, Soteropoulos P, Lukac DM
Submission date May 09, 2008
Last update date Aug 30, 2008
Contact name David M. Lukac
E-mail(s) lukacdm@njms.rutgers.edu
Phone 973 972-4868
Organization name Rutgers Univ./NJ Medical School
Department Microbiology, Biochemistry and Molecular Genetics
Street address 225 Warren St.; ICPH E350C; PO Box 1709
City Newark
State/province NJ
ZIP/Postal code 07101
Country USA
 
Samples (36) GSM288239, GSM288242, GSM288244, GSM288245, GSM288246, GSM288247 
Series (1)
GSE11432 Direct transcriptional targets of the HHV 8/KSHV Rta Lytic Switch Protein

Data table header descriptions
ID
ORGANISM Organism source of detector oligonucleotide
SEQUENCE Sequence of detector oligonucleotide
Len Length of detector oligonucleotide
RANGE_GB GenBank accession number
RANGE_START Nucleotide start position of detector relative to GenBank accession reference sequence
RANGE_END Nucleotide end position of detector relative to GenBank accession reference sequence
RANGE_STRAND Oligonucleotide strand represented by detector
GI GenBank identifier
ORF Open reading frame designator
SPOT ID Non-coding RNA designator

Data table
ID ORGANISM SEQUENCE Len RANGE_GB RANGE_START RANGE_END RANGE_STRAND GI ORF SPOT ID
1_K1(conserved) Human herpesvirus 8 CGGCCCTTGTGTAAACCTGTCTTTCAGACCTTGTTGGACATCCTGTACAATCAAGATGTTCCTGT 65 U75698.1 50 114 + 2065526 K1
10_ORF11 Human herpesvirus 8 GAATGGCGCCCAAACAAGCCAGCACCCCTGAAACTGGTGAACACGAGTGATCATCCCGTCATATT 65 U75698.1 16774 16838 + 2065526 ORF 11
100_PAN-AS Human herpesvirus 8 GGGAAAAGTAGGACGGAAAACCTAGCCGAAAGCCAGGATGGGTATATTGCCAAAAGCG 58 U75698.1 28839 28782 - 2065526 Antisense to nut-1/PAN
101_UPPAN-A Human herpesvirus 8 CCAACGGGGTCCTCAGGTGGTATTTCCGGAAGCATTACCAAATAAGGCAACCTCAGCTGGGAATA 65 U75698.1 23732 23796 + 2065526 Upstream of nut-1/PAN A
102_UPPAN-B Human herpesvirus 8 CCCTCGCGCACTGCGCGCGCGGCGGCACGTGGGACGGATCTCTTGGATTTACCCGTAACGAGGAGCCCCG 70 U75698.1 24225 24294 + 2065526 Upstream of nut-1/PAN B
103_UPPAN-C Human herpesvirus 8 GATGAGGCGGAAGCATATCCCGCTTCCAGCGAACGGAAATAAGAATCATCCGTTCCAGCATTTATTCA 68 U75698.1 25197 25264 + 2065526 Upstream of nut-1/PAN C
104_UPPAN-D Human herpesvirus 8 CCGTCCGCCCTACTGTCGCTATCCCGCCTTGACAGATGTCTAACGTATTCACGGACGCC 59 U75698.1 26557 26615 + 2065526 Upstream of nut-1/PAN D
105_UPPAN-E Human herpesvirus 8 CAGGGGTCATCTGGCGATCAGTGTACCATATTCCCACGACCCATCAACACCGCTGCTTGAG 61 U75698.1 27813 27873 + 2065526 Upstream of nut-1/PAN E
106_UPPAN-F Human herpesvirus 8 GTGTTGGCGGGTTTGACCACGGTTACTGATAGGTAGACGAGTCCGACAATCACACACGTC 60 U75698.1 28163 28222 + 2065526 Upstream of nut-1/PAN F
11_K2 Human herpesvirus 8 GACATACAGGAAGAGCTCAATAAGCTGACTAAGACGCACTACAGTCCACCCAAATTTGACCGCGG 65 U75698.1 17473 17409 - 2065526 K2
12_ORF2 Human herpesvirus 8 TTTTAACCCGGGTTTTACATGACTTTGCGTGTGACGTGTTTCTCTCGCATGATAGCTTGGCTGCG 65 U75698.1 18153 18089 - 2065526 ORF 2
13_K3 Human herpesvirus 8 TAGTGTCTCCTGCCATAATAAGGCTGGACCCTCCTCTCTAGTTGATATCCTTCCACAGGGTTTGC 65 U75698.1 18746 18682 - 2065526 K3
14_ORF70 Human herpesvirus 8 TGACGGTGAGCTTTCCTGTCAGCTGTATCAGAGGTCGGGAGACATGGGTTTGGGAGTTCCTTTTA 65 U75698.1 20421 20357 - 2065526 ORF 70
15_K4 Human herpesvirus 8 TCCTGGCATAGACCGGACAAGTGCTGTCTCGGTTACCAGAAAAGACCATTACCACAGGTGCTTCT 65 U75698.1 21754 21690 - 2065526 ORF K4
16_K4_1 Human herpesvirus 8 GATAAGCTGATATGCGGGTGGTACTGGACGTCCACCGTGTATTGTCGCCAGAAGGCAGTCATTTT 65 U75698.1 22382 22318 - 2065526 K4.1
17_K4_2 Human herpesvirus 8 TTTTGGACCGTGGGAAATGGGACCGGTGTCCTCTCTATGACCTTTTCAGTCACCTTGCCACCTCG 65 U75698.1 23095 23031 - 2065526 K4.2
173_H200007830 Homo sapiens TGAAGAGGGGAGGGGCCTAGGGAGCCGCACCTTGTCATGTACCATCAATAAAGTACCCTGTGCTCAACC 69 NG_007073.2 8812 8880 + 163954974 GAPDH
18_K5 Human herpesvirus 8 ACGAGTCATCTGAAGGAGACGTCGCCTCTGGAGACAAAGAACGTGACGGTTCATCCGGAGACGAG 65 U75698.1 25888 25824 - 2065526 K5
19_K6 Human herpesvirus 8 CGTCCACGTTTTATGCTGCGTTAGCGTACTGCTTGCCACGTTTTACCTGACGCCCACAGAAAGCG 65 U75698.1 27416 27352 - 2065526 K6
2_K1(subgroupB) Human herpesvirus 8 GGACTCAGCTTCACCGAATAACGGCGTCTAACCTAACTGTTTCTTCGCTCACCTGCAATTTTACT 65 AF133040.1 265 329 + 4836707 K1-B

Total number of rows: 107

Table truncated, full table size 14 Kbytes.




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