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Sample GSM345416 Query DataSets for GSM345416
Status Public on Dec 04, 2008
Title Pho2 40nM DIP-chip Replicate A
Sample type genomic
 
Channel 1
Source name MBP-Pho2DBD 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 MBPPho2DBD 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 MBPPho2DBD 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 -0.298198700706158
seq_id=CHR1;probe_id=CHR100P000124753;count=1 0.604456825755726
seq_id=CHR1;probe_id=CHR100P000001996;count=1 0.145069638181374
seq_id=CHR1;probe_id=CHR100P000011261;count=1 2.35335190827563
seq_id=CHR1;probe_id=CHR100P000130876;count=1 -1.36204271403624
seq_id=CHR1;probe_id=CHR100P000056688;count=1 -1.12831940807735
seq_id=CHR1;probe_id=CHR100P000162897;count=1 -0.564159704038677
seq_id=CHR1;probe_id=CHR100P000137475;count=1 1.40233983575328
seq_id=CHR1;probe_id=CHR100P000065072;count=1 0.539981431008448
seq_id=CHR1;probe_id=CHR100P000012733;count=1 1.35398328969283
seq_id=CHR1;probe_id=CHR100P000206347;count=1 -1.45069638181374
seq_id=CHR1;probe_id=CHR100P000098462;count=1 0.50774373363481
seq_id=CHR1;probe_id=CHR100P000139716;count=1 -0.822061283027787
seq_id=CHR1;probe_id=CHR100P000161361;count=1 2.30499536221517
seq_id=CHR1;probe_id=CHR100P000020447;count=1 0.193426184241832
seq_id=CHR1;probe_id=CHR100P000005358;count=1 1.50711235221761
seq_id=CHR1;probe_id=CHR100P000189988;count=1 1.4990529278742
seq_id=CHR1;probe_id=CHR100P000207435;count=1 -1.08802228636031
seq_id=CHR1;probe_id=CHR100P000212203;count=1 0.322376973736387
seq_id=CHR1;probe_id=CHR100P000210763;count=1 0.0161188486868194

Total number of rows: 378684

Table truncated, full table size 23891 Kbytes.




Supplementary file Size Download File type/resource
GSM345416_194495_Pho2_40nMaMed_532.pair.gz 6.8 Mb (ftp)(http) PAIR
GSM345416_194495_Pho2_40nMaMed_532.tif.gz 15.9 Mb (ftp)(http) TIFF
GSM345416_194495_Pho2_40nMaMed_635.pair.gz 6.7 Mb (ftp)(http) PAIR
GSM345416_194495_Pho2_40nMaMed_635.tif.gz 15.5 Mb (ftp)(http) TIFF
GSM345416_194495_Pho2_40nMaMed_635_ratio.gff.gz 5.1 Mb (ftp)(http) GFF
Processed data included within Sample table
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