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Series GSE60200 Query DataSets for GSE60200
Status Public on Mar 01, 2015
Title Quantitative modeling of transcription factor binding specificities using DNA shape
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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)
Overall design Two rounds of SELEX were performed on Max protein as described in Slattery et al, Cell, 2011 (PMID 22153072). Briefly, His-tagged Max was incubated with a randomized 16mer oligonucleotide library (GTTCAGAGTTCTACAGTCCGACGATCTGG[ACGT]{16}CCAGAACTCGTATGCCGTCTTCTGCTTG). Max bound DNA was amplified and sequenced as described (Slattery et al, 2011).
Contributor(s) Mann RS, Bussemaker HJ, Gordân R
Citation(s) 25775564
Submission date Aug 07, 2014
Last update date May 15, 2019
Contact name Namiko Abe
Phone 212-305-2111
Organization name Columbia University
Department Biochemistry and Molecular Biophysics
Lab Richard Mann
Street address 701 W. 168th St HHSC1104
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (1)
GSM1467529 Human Max protein
BioProject PRJNA257744
SRA SRP045333

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Supplementary file Size Download File type/resource
GSE60200_Max_selex_normalized.txt.gz 251.8 Kb (ftp)(http) TXT
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