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Sample GSM345432 Query DataSets for GSM345432
Status Public on Dec 04, 2008
Title Swi5 40nM DIP-chip Replicate B
Sample type genomic
 
Channel 1
Source name MBP-Swi5DBD 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 MBPSwi5DBD 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 Cy3
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 Cy5
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 MBPSwi5DBD 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 0.510975202068749
seq_id=CHR1;probe_id=CHR100P000124753;count=1 -0.638719002585937
seq_id=CHR1;probe_id=CHR100P000001996;count=1 0.229938840930937
seq_id=CHR1;probe_id=CHR100P000011261;count=1 1.12414544455125
seq_id=CHR1;probe_id=CHR100P000130876;count=1 -0.664267762689374
seq_id=CHR1;probe_id=CHR100P000056688;count=1 0.638719002585937
seq_id=CHR1;probe_id=CHR100P000162897;count=1 -1.99280328806812
seq_id=CHR1;probe_id=CHR100P000137475;count=1 -0.408780161654999
seq_id=CHR1;probe_id=CHR100P000065072;count=1 0.689816522792812
seq_id=CHR1;probe_id=CHR100P000012733;count=1 -1.66066940672344
seq_id=CHR1;probe_id=CHR100P000206347;count=1 -1.0219504041375
seq_id=CHR1;probe_id=CHR100P000098462;count=1 -0.30658512124125
seq_id=CHR1;probe_id=CHR100P000139716;count=1 1.45627932589594
seq_id=CHR1;probe_id=CHR100P000161361;count=1 -1.0219504041375
seq_id=CHR1;probe_id=CHR100P000020447;count=1 0.332133881344687
seq_id=CHR1;probe_id=CHR100P000005358;count=1 -1.48182808599937
seq_id=CHR1;probe_id=CHR100P000189988;count=1 -2.52932725024031
seq_id=CHR1;probe_id=CHR100P000207435;count=1 -0.638719002585937
seq_id=CHR1;probe_id=CHR100P000212203;count=1 0.0766462803103124
seq_id=CHR1;probe_id=CHR100P000210763;count=1 1.8395107274475

Total number of rows: 378684

Table truncated, full table size 23839 Kbytes.




Supplementary file Size Download File type/resource
GSM345432_219435_S5040B_Med_532.pair.gz 6.7 Mb (ftp)(http) PAIR
GSM345432_219435_S5040B_Med_532.tif.gz 4.2 Mb (ftp)(http) TIFF
GSM345432_219435_S5040B_Med_532_ratio.gff.gz 4.9 Mb (ftp)(http) GFF
GSM345432_219435_S5040B_Med_635.pair.gz 6.7 Mb (ftp)(http) PAIR
GSM345432_219435_S5040B_Med_635.tif.gz 4.1 Mb (ftp)(http) TIFF
Processed data included within Sample table
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