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Sample GSM1052392 Query DataSets for GSM1052392
Status Public on Dec 13, 2012
Title pTH3855_ME_8mer
Sample type protein
 
Source name Foxp1_ME design
Organism synthetic construct
Characteristics dbd: Fork_head
platform_id_id design: ME
Extracted molecule protein
Extraction protocol We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.
Label Cy5
Label protocol DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as SacI–BamHI fragments into pTH5325, a modified T7-driven GST expression vector.
 
Hybridization protocol We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate. After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.
Scan protocol The array was imaged using an Agilent microarray scanner at 2 mM resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low). The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).
Data processing We provide several scores for each 8-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots. Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.
 
Submission date Dec 12, 2012
Last update date Dec 13, 2012
Contact name Matthew Tyson Weirauch
E-mail(s) matthew.weirauch@cchmc.org
Organization name Cincinnati Children's Hospital
Street address 3333 Burnet Avenue
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL11260
Series (1)
GSE42864 Evaluation of methods for modeling transcription factor sequence specificity

Data table header descriptions
ID_REF
VALUE median intensity for the 8mer sequence
E-Score
Z-Score

Data table
ID_REF VALUE E-Score Z-Score
AAAAAAAA 10091.621 0.0225306812443742 0.384631470576371
AAAAAAAC 12585.1381 0.27084537939651 2.52507124186275
AAAAAAAG 10091.621 -0.106892051053386 0.384631470576371
AAAAAAAT 11139.8339 0.138618104688158 1.28441939660881
AAAAAACA 15086.7016 0.385546334716459 4.67241805805195
AAAAAACC 9929.03415 -0.0257943137739166 0.245066612557883
AAAAAACG 9435.0732 0.0506894830437088 -0.178950396526353
AAAAAACT 9907.67575 0.0818623899536762 0.226732521802684
AAAAAAGA 9372.7617 -0.0696317645896648 -0.232438705392779
AAAAAAGC 10946.83835 0.17962798305122 1.11875165328302
AAAAAAGG 9889.3535 -0.110805863466651 0.211004667921331
AAAAAAGT 10097.17525 0.0331541557101971 0.38939924922913
AAAAAATA 12356.2841 0.252801927594459 2.32862253757354
AAAAAATC 9229.3505 -0.127525553340965 -0.355543149363868
AAAAAATG 10434.52095 0.0773177417761533 0.678977432973064
AAAAAATT 10923.2861 0.0579160567525617 1.09853435755912
AAAAACAA 18580.37885 0.441253246736364 7.67139718433844
AAAAACAC 13037.6103 0.328967156249314 2.9134742298677
AAAAACAG 14288.6606 0.365131550273851 3.9873781617877
AAAAACAT 16094.2036 0.383485367406529 5.53725967090898

Total number of rows: 32896

Table truncated, full table size 1819 Kbytes.




Supplementary file Size Download File type/resource
GSM1052392_pTH3855_ME.raw.txt.gz 1.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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