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Series GSE26767 Query DataSets for GSE26767
Status Public on Apr 28, 2011
Title A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity
Organism synthetic construct
Experiment type Other
Summary We examine the use of high-throughput sequencing on binding sites recovered using a bacterial one-hybrid (B1H) system and find that improved models of transcription factor (TF) binding specificity can be obtained compared to standard methods of sequencing a small subset of the selected clones. We can obtain even more accurate binding models using a modified version of B1H selection method with constrained variation (CV-B1H). However, achieving these improved models using CV-B1H data required the development of a new method of analysis - GRaMS (Growth Rate Modeling of Specificity) - that estimates bacterial growth rates as a function of the quality of the recognition sequence. We benchmark these different methods of motif discovery using Zif268, a well characterized C2H2 zinc finger transcription factor on both a 28bp randomized library for the standard B1H method and on 6bp randomized library for the CV-B1H method for which forty-five different experimental conditions were tested: 5 time points and three different IPTG and 3-AT concentrations. We find that GRaMS analysis is robust to the different experimental parameters whereas other analysis methods give widely varying results depending on the conditions of the experiment. Finally, we demonstrate that the CV-B1H assay can be performed in liquid media, which produces recognition models that are similar in quality to sequences recovered from selection on solid media.
Overall design All selections were performed using the bait transcription factor Zif268. 45 different B1H selections were performed on plates and the selected sites were multiplexed and sequenced in a single lane. A single selection was performed in liquid media and sequenced along with other multiplexed sets of sites in a separate lane. For the experiments performed on plates, the of the selections assays was varied (4, 8, 12, 18, 24 hours). The stringency of the selections was also varied by changing the concentration of IPTG (0, 10, 50 uM) and 3-AT (0.5, 1, 2 mM). The initial randomized library used for all selections was also sequenced in a single lane. The randomized portion of each transcription factor binding site is 6bp long and is immediately 5' of the constant sequence, GCGG, which is the consensus binding site for finger 1 of Zif268. Upstream of the randomized binding site is a 4bp randomized region referred to as the key region. The purpose of the key region is to detect possible PCR 'jackpotting.' The single liquid media experiment was run for 4 hours using 50uM IPTG and 5mM 3-AT. Four selections were performed using a prey library with a 28bp long randomized region and not fixed consensus site region. These selections were performed at either 36 or 48 hours using 10uM IPTG and 0, 2, or 5 mM 3-AT.
Web link
Contributor(s) Wolfe SA, Stormo GD
Citation(s) 21507886
Submission date Jan 20, 2011
Last update date May 15, 2019
Contact name Scot Wolfe
Organization name UMass Medical School
Department MCCB
Street address 364 Plantation Street, LRB 619
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
Platforms (1)
GPL11631 Illumina Genome Analyzer IIx (synthetic construct)
Samples (53)
GSM658818 4hrs_0μM_IPTG_0.5mM_3-AT_plates
GSM658819 4hrs_0μM_IPTG_1mM_3-AT_plates
GSM658820 4hrs_0μM_IPTG_2mM_3-AT_plates
SRA SRP005928
BioProject PRJNA136293

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