GEO DataSets

(Submitter supplied) The E2F family of transcription factors is typically described as binding the family consensus sequence TTTSSCGC, were S is G or C. Analysis of ChIP-seq experiments, however, reveals that this consensus sequence is found in only 10% of ChIP-seq peaks, suggesting that the mechanism for E2F sequence recognition cannot be explained using previous assumptions. In order to better understand E2F sequence specificity, we performed high-throughput Universal Protein Binding Microarray experiments to obtain the relative binding affinity for every possible 8-mer, as well a large number of bound and unbound probes intheir native genomic sequence context. more...

Organism:

synthetic construct; Homo sapiens

Type:

Other

Platform:

GPL19244

3 Samples

Download data: GPR, TXT

(Submitter supplied) Until now, it has been reasonably assumed that specific base-pair recognition is the only mechanism controlling the specificity of transcription factor (TF)−DNA binding. Contrary to this assumption, here we show that nonspecific DNA sequences possessing certain repeat symmetries, when present outside of specific TF binding sites (TFBSs), statistically control TF−DNA binding preferences. We used high-throughput protein−DNA binding assays to measure the binding levels and free energies of binding for several human TFs to tens of thousands of short DNA sequences with varying re- peat symmetries. more...

Organism:

synthetic construct; Homo sapiens

Type:

Other

Platform:

GPL19252

4 Samples

Download data: GPR, TXT

(Submitter supplied) Accurate predictions of the DNA binding specificities of transcription factors (TFs) are necessary for understanding gene regulatory mechanisms. Traditionally, predictive models are built based on nucleotide sequence features. Here, we employed three- dimensional DNA shape information obtained on a high-throughput basis to integrate intuitive DNA structural features into the modeling of TF binding specificities using support vector regression. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by array

Platform:

GPL17173

3 Samples

Download data: TXT

(Submitter supplied) The SELEX-seq platform was used to generate DNA-binding affinity predictions for the human Max transcription factor. This experiment was performed as part of a cross-validation study comparing the accuracy of DNA shape-augmented TF binding specificity models across two different platforms (SELEX-seq and gcPBM)

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

1 Sample

Download data: TXT

(Submitter supplied) The forkhead transcription factor (TF) FoxN3 recognizes both the canonical forkhead DNA motif (RYAAAYA), as well as a novel alternate motif (GACGC). These two motifs are more distinct than the typically observed primary and secondary motifs of other TFs, as the two motifs cannot be aligned and are not clearly related to each other. Amino acids at the canonical base-contacting positions in the forkhead DNA binding domain are largely conserved throughout the forkhead family, so the ability of FoxN3 and other bispecific forkhead factors to recognize the alternate site cannot be explained by amino acid substitutions at these positions. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: NARROWPEAK

(Submitter supplied) Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae transcription factors but a comprehensive evaluation of their data has been lacking. Results: We analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. more...

Organism:

synthetic construct; Saccharomyces cerevisiae

Type:

Other

Platform:

GPL6796

27 Samples

Download data

(Submitter supplied) Transcription factors (TFs) are primary regulators of gene expression in cells, where they bind specific genomic target sites to control transcription. Quantitative measurements of TF-DNA binding energies can improve the accuracy of predictions of TF occupancy and downstream gene expression in vivo and shed light on how transcriptional networks are rewired throughout evolution. Here, we present a novel sequencing-based TF binding assay and analysis pipeline (BET-seq, for Binding Energy Topography by sequencing) capable of providing quantitative estimates of binding energies for more than one million DNA sequences in parallel at high energetic resolution. more...

Organism:

synthetic construct

Type:

Other

Platforms:

GPL17769 GPL19424

14 Samples

Download data: TXT

(Submitter supplied) Genomic analyses often involve scanning for potential transcription-factor (TF) binding sites using models of the sequence specificity of DNA binding proteins. Many approaches have been developed to model and learn a protein’s binding specificity by representing sequence motifs, including the gaps and dependencies between binding-site residues, but these methods have not been systematically compared. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL11260

172 Samples

Download data: TXT

(Submitter supplied) Transcription factors (TF) recognize specific genomic sequences to regulate complex gene expression programs. Although it is well established that TFs bind specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood. Many DNA-binding proteins induce changes in the DNA structure outside the intrinsic B-DNA envelope. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL29076

1 Sample

Download data: TXT

(Submitter supplied) Transcription factors (TF) recognize specific genomic sequences to regulate complex gene expression programs. Although it is well established that TFs bind specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood. Many DNA-binding proteins induce changes in the DNA structure outside the intrinsic B-DNA envelope. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL29075

3 Samples

Download data: TXT

(Submitter supplied) Transcription factors (TF) recognize specific genomic sequences to regulate complex gene expression programs. Although it is well established that TFs bind specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood. Many DNA-binding proteins induce changes in the DNA structure outside the intrinsic B-DNA envelope. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL29074

6 Samples

Download data: TXT

(Submitter supplied) Transcription factors (TF) recognize specific genomic sequences to regulate complex gene expression programs. Although it is well established that TFs bind specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood. Many DNA-binding proteins induce changes in the DNA structure outside the intrinsic B-DNA envelope. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL29073

7 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae; synthetic construct; Homo sapiens

Type:

Protein profiling by protein array

6 related Platforms

29 Samples

Download data: TXT

(Submitter supplied) Transcription factors (TF) recognize specific genomic sequences to regulate complex gene expression programs. Although it is well established that TFs bind specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood. Many DNA-binding proteins induce changes in the DNA structure outside the intrinsic B-DNA envelope. more...

Organism:

synthetic construct

Type:

Protein profiling by protein array

Platform:

GPL29030

4 Samples

Download data: TXT

(Submitter supplied) Transcription factors (TF) recognize specific genomic sequences to regulate complex gene expression programs. Although it is well established that TFs bind specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly understood. Many DNA-binding proteins induce changes in the DNA structure outside the intrinsic B-DNA envelope. more...

Organism:

Homo sapiens; Saccharomyces cerevisiae; synthetic construct

Type:

Other

Platform:

GPL29025

8 Samples

Download data: TXT

(Submitter supplied) The first 18 experiments are ordered according to the legend in Figure 3 of the published paper. Experiment 19 is the gene expression profile of the swi4 deletion strain compared to the wild-type strain. This study is described in more detail in Iyer VR, et al.(2001) Nature 409:533-38 Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL49 GPL65 GPL50

19 Samples

Download data

(Submitter supplied) The purpose of this experiment was to identify the genes with increased expression during sporulation in wild-type P. pastoris, and during sporulation in cells with Ndt80 deleted. Cells were grown unti log-phase in YPD or in sporulation media (0.5% sodium acetate, 1% potassium chloride, 1% glucose, 2% agar plates ) for 30 hours. Each experiment was repeated three times and sequenced on an Illumina HiSeq 4000

Organism:

Komagataella pastoris

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22717 GPL22842

9 Samples

Download data: GTF

(Submitter supplied) The purpose of this experiment was to identify the genes bound by the two Ndt80 paralogs in C. albicans when constitutively expressed, and for Ndt80B when endogenously expressed. Both paralogs were tagged with c-myc, and the protein was immunoprecipitated with a c-myc antibody. For constitutive expression, each native Ndt80 promoter was replaced by the C. albicans Tdh3 promoter. Cells were grown unti log-phase in YPD. more...

Organism:

Candida albicans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19036

8 Samples

Download data: WIG, XLS

(Submitter supplied) The purpose of this experiment was to identify the genes bound by the two Ndt80 paralogs in S. stipitis when constitutively expressed. Both paralogs were tagged with c-myc, the native Ndt80 promoter was replaced with the E. gossypii Tef1 promoter and the protein was immunoprecipitated with a c-myc antibody. Cells were grown unti log-phase in YPD. Each experiment was repeated twice and sequenced on an Illumina HiSeq 2500.

Organism:

Scheffersomyces stipitis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22718

6 Samples

Download data: WIG, XLS

(Submitter supplied) The purpose of this experiment was to identify the genes bound by Ndt80 in P. pastoris when constitutively expressed. Ndt80 was tagged with c-myc, the native Ndt80 promoter was replaced with the E. gossypii Tef1 promoter and the protein was immunoprecipitated with a c-myc antibody. Cells were grown unti log-phase in YPD. Each experiment was repeated twice and sequenced on an Illumina HiSeq 2500.

Organism:

Komagataella pastoris

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22717

4 Samples

Download data: WIG, XLS