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Series GSE178811 Query DataSets for GSE178811
Status Public on Apr 26, 2023
Title DNA Binding Specificities of Fkh1, Fkh2, Hcm1, and Fhl1 Revealed by SELEX-seq
Organism synthetic construct
Experiment type Other
Summary Quantifying the preferences of DNA binding proteins is an essential step in determining how transcription factors (TFs) interact with their targets in the genome. High-throughput in vitro binding assays have been used to identify the inherent DNA preferences of TFs in a controlled environment isolated from confounding factors such as genome accessibility, DNA methylation, and TF binding cooperativity. Unfortunately, the limited variable region or sequencing depth typically utilized by many of the available experimental approaches makes it difficult to measure the preferences of moderate- to low-affinity binding sites, and impossible to measure small-scale differences between closely related homologs. The Forkhead box (FOX) family of TFs is known to play a crucial role in regulating a variety of key processes from proliferation and development, to tumor suppression and aging. By using the high-sequencing depth SELEX-seq approach to study all four FOX homologs in Saccharomyces cerevisiae, we have been able to precisely quantify the contribution and importance of nucleotide positions flanking the core of the binding sites. Essential to this process was the alignment of our SELEX-seq reads to a set of candidate core sequences determined by two newly developed strategies of alignment and reprioritization applied to enriched k-mers.
Overall design SELEX-seq was performed on Fkh1, Fkh2, Hcm1, and Fhl1 constructs as described in Cooper et al. (to be submitted). We provide sequencing results for both the intial library (R0) as well as the selected libraries after one (R1) or two (R2) rounds of selection. A test experiment was performed using just the Fkh1 construct with a shallower depth of sequencing. The final, large-scale experiments were performed on both all constructs. The initial libraries included a 16 bp randomized region flanked by two fixed adapters absent of any known binding site for the used transcription factors.
Web link
Contributor(s) Rohs R, Cooper BH, Machado AC, Gan Y, Aparicio O
Citation(s) 37177995
Submission date Jun 24, 2021
Last update date Jul 26, 2023
Contact name Remo Rohs
Organization name University of Southern California
Department Quantitative and Computational Biology
Lab Rohs Lab
Street address 1050 Childs Way
City Los Angeles
State/province CA
ZIP/Postal code 90089
Country USA
Platforms (2)
GPL19424 Illumina NextSeq 500 (synthetic construct)
GPL19604 Illumina HiSeq 2500 (synthetic construct)
Samples (13)
GSM5398236 R0_test
GSM5398237 Fkh1_R1_test
GSM5398238 Fkh1_R2_test
BioProject PRJNA741127
SRA SRP325475

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE178811_RAW.tar 495.1 Mb (http)(custom) TAR (of TAR)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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