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Sample GSM345418 Query DataSets for GSM345418
Status Public on Dec 04, 2008
Title Pho4 40nM DIP-chip Replicate A
Sample type genomic
 
Channel 1
Source name MBP-Pho4DBD DIP DNA
Organism Saccharomyces cerevisiae
Characteristics Genomic DNA isolated by CsCl prep from S288C strain, sheared to avg size of 600bp, and then used for DIP-chip with 40nM MBPPho4DBD purified from E. coli.
Biomaterial provider Andrea J Gossett
Extracted molecule genomic DNA
Extraction protocol Cold Spring Harb. Protoc.; 2008; doi:10.1101/pdb.prot4972
Amplified by Invitrogen WGA protocol
Label Cy5
Label protocol NimbleGen amplification and labeling
 
Channel 2
Source name S288C Genomic DNA
Organism Saccharomyces cerevisiae
Characteristics Genomic DNA isolated by CsCl prep from S288C strain, sheared by sonication to avg size of 600bp
Biomaterial provider Andrea J Gossett
Extracted molecule genomic DNA
Extraction protocol CsCl Prep
Label Cy3
Label protocol NimbleGen amplification and labeling
 
 
Hybridization protocol Competitively hybed ~10ug channel 1 and 2 DNA on NimbleGen 385k whole genome arrays using Maui SL mixers in Maui hybridization chamber. Washed as per NimbleGen hybridization protocol.
Scan protocol Scanned on GenePix 4000B scanner as per NimbleGen protocol
Description DIP-chip done using MBPPho4DBD competitively hybridized against whole genome S288C DNA on NimbleGen 385k feature arrays.
As in DIP-chip: rapid and accurate determination of DNA-binding specificity. Liu X, Noll DM, Lieb JD, Clarke ND. Genome Res. 2005. 15: 421-427
Data processing Raw log2 ratio for experiments (obtained from GFF output file from NimbleScan) was median-center z-scored.
 
Submission date Nov 25, 2008
Last update date Dec 03, 2008
Contact name Jason D Lieb
E-mail(s) jlieb@bio.unc.edu
Phone 919-843-3228
URL http://www.bio.unc.edu/faculty/lieb/labpages/default.shtml
Organization name University of North Carolina at Chapel Hill
Department Biology
Lab Jason Lieb
Street address 203 Fordham Hall
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL7699
Series (1)
GSE13751 DIP-chip from Cbf1, Leu3, Pho2, Pho4, Rap1, Rox1, and Swi5

Data table header descriptions
ID_REF
VALUE Z-scored log2ratio of DIP-chip DNA/genomic DNA

Data table
ID_REF VALUE
seq_id=CHR1;probe_id=CHR100P000123281;count=1 -0.878907443894886
seq_id=CHR1;probe_id=CHR100P000124753;count=1 0.549317152434304
seq_id=CHR1;probe_id=CHR100P000001996;count=1 -0.219726860973721
seq_id=CHR1;probe_id=CHR100P000011261;count=1 -0.0941686547030235
seq_id=CHR1;probe_id=CHR100P000130876;count=1 2.11879473081803
seq_id=CHR1;probe_id=CHR100P000056688;count=1 -0.062779103135349
seq_id=CHR1;probe_id=CHR100P000162897;count=1 2.16587905816954
seq_id=CHR1;probe_id=CHR100P000137475;count=1 -0.533622376650466
seq_id=CHR1;probe_id=CHR100P000065072;count=1 -0.847517892327211
seq_id=CHR1;probe_id=CHR100P000012733;count=1 1.11432908065244
seq_id=CHR1;probe_id=CHR100P000206347;count=1 -0.769044013408025
seq_id=CHR1;probe_id=CHR100P000098462;count=1 0.0470843273515117
seq_id=CHR1;probe_id=CHR100P000139716;count=1 -1.34975071741
seq_id=CHR1;probe_id=CHR100P000161361;count=1 -1.49100369946454
seq_id=CHR1;probe_id=CHR100P000020447;count=1 -0.17264253362221
seq_id=CHR1;probe_id=CHR100P000005358;count=1 -0.0156947757838372
seq_id=CHR1;probe_id=CHR100P000189988;count=1 2.00893130033117
seq_id=CHR1;probe_id=CHR100P000207435;count=1 -0.674875358705002
seq_id=CHR1;probe_id=CHR100P000212203;count=1 0.235421636757559
seq_id=CHR1;probe_id=CHR100P000210763;count=1 -0.251116412541396

Total number of rows: 378684

Table truncated, full table size 23865 Kbytes.




Supplementary file Size Download File type/resource
GSM345418_175580_P4040AMed_532.pair.gz 6.7 Mb (ftp)(http) PAIR
GSM345418_175580_P4040AMed_532.tif.gz 4.1 Mb (ftp)(http) TIFF
GSM345418_175580_P4040AMed_635.pair.gz 6.6 Mb (ftp)(http) PAIR
GSM345418_175580_P4040AMed_635.tif.gz 4.1 Mb (ftp)(http) TIFF
GSM345418_175580_P4040AMed_635_ratio.gff.gz 5.0 Mb (ftp)(http) GFF
Processed data included within Sample table
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