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Platform GPL3703 Query DataSets for GPL3703
Status Public on Aug 11, 2006
Title Lieb Lab at UNC-CH_Yeast Oligo Tiling Array from (RandoLab_Harvard)
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Saccharomyces cerevisiae
Manufacturer Center for Genomics Research, Harvard University
Manufacture protocol MGuide, www.microarrays.org
Support glass
Coating poly-L-lysine
 
Description The sequence from S. cerevisiae chromosome III was fragmented into 50-mers overlapping every 20 base pairs. Potentially cross-hybridizing probes were filtered by BLASTing these sequences against the entire genome and eliminating sequences from chromosome III that included 5 or more contiguous probes with perfect BLAST matches, leaving 30 contigs covering 278,960 base pairs. Oligonucleotides were also tiled over one kilobase of 230 promoters on other chromosomes, starting at -900 from the start codon and extending to +100.
 
Contributor(s) Rando O, Hogan GJ
Submission date Apr 25, 2006
Last update date Oct 24, 2011
Contact name Jason D Lieb
E-mail(s) jlieb@bio.unc.edu
Phone 919-842-3228
Organization name University of North Carolina at Chapel Hill
Department Department of Biology
Lab Jason Lieb
Street address 203 Fordham Hall
City Chapel Hill
State/province NC
ZIP/Postal code 27599-3280
Country USA
 
Samples (4) GSM106580, GSM106581, GSM106582, GSM106583
Series (2)
GSE4721 Yeast FAIRE_BY4741 on Oligo Arrays
GSE4736 Yeast FAIRE Study_Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters.

Data table header descriptions
ID assigned as in Yuan et al., 2005
SEQUENCE nucleotide sequences of the 50mer oligo probes on tiled yeast nucleosome array
CHROMOSOME
START COORDINATE
STOP COORDINATE
SPOT_ID CHROMOSOME[START..STOP]

Data table
ID SEQUENCE CHROMOSOME START COORDINATE STOP COORDINATE SPOT_ID
493550 CACGCTGTGGTTCCCACCGCACGCTATCTTCCTGACTATTGCTCCATCAT 1 114471 114520 Chr1[114471..114520]
493552 ACGCTATCTTCCTGACTATTGCTCCATCATCTCCTGGCACAGACCTCTGT 1 114491 114540 Chr1[114491..114540]
493554 GCTCCATCATCTCCTGGCACAGACCTCTGTGGGGTATCCATATCCTCATC 1 114511 114560 Chr1[114511..114560]
493556 AGACCTCTGTGGGGTATCCATATCCTCATCGTGCCCCAGTCCCAGTTGCC 1 114531 114580 Chr1[114531..114580]
493558 TATCCTCATCGTGCCCCAGTCCCAGTTGCCTTTGCCCATTAGACCCAAAC 1 114551 114600 Chr1[114551..114600]
493560 CCCAGTTGCCTTTGCCCATTAGACCCAAACGCATACACACAACTCATCGA 1 114571 114620 Chr1[114571..114620]
493562 AGACCCAAACGCATACACACAACTCATCGATACAAGCCTGTTATAGCCTT 1 114591 114640 Chr1[114591..114640]
493564 AACTCATCGATACAAGCCTGTTATAGCCTTTAATGATCACATTCCATCAC 1 114611 114660 Chr1[114611..114660]
493566 TTATAGCCTTTAATGATCACATTCCATCACTTGCGCTTTGGATCTGCCTG 1 114631 114680 Chr1[114631..114680]
493568 ATTCCATCACTTGCGCTTTGGATCTGCCTGCATTATCAAGGCTCAAACGG 1 114651 114700 Chr1[114651..114700]
493570 GATCTGCCTGCATTATCAAGGCTCAAACGGCTGCGTTACCCCCGTCGCCG 1 114671 114720 Chr1[114671..114720]
493572 GCTCAAACGGCTGCGTTACCCCCGTCGCCGCGAAATTTTTCATAATTTTT 1 114691 114740 Chr1[114691..114740]
493574 CCCGTCGCCGCGAAATTTTTCATAATTTTTCACTTTGTAGGATTAAAAGA 1 114711 114760 Chr1[114711..114760]
493576 CATAATTTTTCACTTTGTAGGATTAAAAGAGATCATGAGCCCATCTCGCA 1 114731 114780 Chr1[114731..114780]
493578 GATTAAAAGAGATCATGAGCCCATCTCGCAATGCAACACGTAACTTAAAT 1 114751 114800 Chr1[114751..114800]
493580 CCATCTCGCAATGCAACACGTAACTTAAATCAGTACTGGCGTGTGCTATA 1 114771 114820 Chr1[114771..114820]
493582 TAACTTAAATCAGTACTGGCGTGTGCTATAGTGCTCTATATTCGAGTTTG 1 114791 114840 Chr1[114791..114840]
493584 GTGTGCTATAGTGCTCTATATTCGAGTTTGTTGCTACTGGTGGACACCCG 1 114811 114860 Chr1[114811..114860]
493586 TTCGAGTTTGTTGCTACTGGTGGACACCCGACTATCTACAGTAAGGAACG 1 114831 114880 Chr1[114831..114880]
493588 TGGACACCCGACTATCTACAGTAAGGAACGTAAACAAGAAAAAGAGAGAA 1 114851 114900 Chr1[114851..114900]

Total number of rows: 24960

Table truncated, full table size 2315 Kbytes.




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

Supplementary file Size Download File type/resource
GPL3703_Rando_OligoArray.gal.gz 571.6 Kb (ftp)(http) GAL

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