NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1052357 Query DataSets for GSM1052357
Status Public on Dec 13, 2012
Title pTH3510_HK_8mer
Sample type protein
 
Source name Esr1_HK design
Organism synthetic construct
Characteristics dbd: zf-C4
platform_id_id design: HK
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 18688.4199 0.27408057671787 1.33518033932947
AAAAAAAC 16169.1337 0.0128788221573834 -0.79206424459456
AAAAAAAG 16691.57565 0.154473347891903 -0.350922698805833
AAAAAAAT 18013.1679 0.0888589721319205 0.765008455014039
AAAAAACA 18582.2441 0.134571210328786 1.24552720841731
AAAAAACC 17626.8984 0.0308945308945309 0.438848726988676
AAAAAACG 17157.0976 -0.00255833813858096 0.0421565181704909
AAAAAACT 19224.71675 0.178629042265406 1.7880207389387
AAAAAAGA 18979.73335 0.239240746552995 1.58116071215759
AAAAAAGC 16853.3969 0.151452887892966 -0.21428344851886
AAAAAAGG 20036.1406 0.246868080201414 2.4731739343872
AAAAAAGT 18351.00775 0.113699098547583 1.05027496865834
AAAAAATA 15583.958 -0.0353651274161931 -1.28617715581082
AAAAAATC 17046.60735 -0.108471347342759 -0.0511396646486417
AAAAAATG 18294.5478 0.179574891696104 1.0026010986367
AAAAAATT 18071.5761 -0.0269023306058991 0.814327395873854
AAAAACAA 18270.1679 0.126770020709415 0.982015104781928
AAAAACAC 17284.8457 -0.0332715635745938 0.150024950836691
AAAAACAG 15159.52585 -0.0308415286083334 -1.64456080921659
AAAAACAT 17638.6816 0.063409139166715 0.448798270784573

Total number of rows: 32896

Table truncated, full table size 1843 Kbytes.




Supplementary file Size Download File type/resource
GSM1052357_pTH3510_HK.raw.txt.gz 1.3 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap