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Series GSE189817 Query DataSets for GSE189817
Status Public on Dec 15, 2021
Title Spec-seq data for ZNF140, ZNF10, ZFP3, ZNF675, ZNF382
Organisms Homo sapiens; synthetic construct
Experiment type Other
Summary This dataset consists of Spec-seq samples data for four tandem zinc finger proteins in human genome, each with two replicates. The Spec-seq is a medium throughput technique to characterize the binding specificity of a TF of interest to thousands of binding sites with resolution down to 0.2kT. Similar samples were deposited to NCBI GEO database before (GSE188166). The data analysis workflow for each ZFP can be accessed through https://github.com/zeropin/ZFPCookbook.
 
Overall design For ZNF140, a truncated construct containing finger 1 to 6 (F1-F6) was fused to N-terminal Halo tag for protein expression and EMSA assay; For ZNF10, F1-F8 construct was used; For ZFP3, F1-F10 construct was used; For ZNF675, both F1-F11 and F1-F6 constructs were tested separately; The DNA library design and experimental workflow was described in a paper to be published in detail. The Spec-seq libraries for ZNF675 includes not only synthetic elements but also 500 endogeneous genomic elements from human genome (300 sites within repeat elements, 200 sites outside repeat elements).
For ZNF382, its DNA-binding domain including 9 fingers was fused to N-terminal HALO-Tag for experimental work. The DNA library design and experimental workflow was described in paper to be published in detail.
 
Contributor(s) Zuo Z
Citation(s) 37680368
Submission date Nov 29, 2021
Last update date Oct 02, 2023
Contact name Zheng Zuo
E-mail(s) zeropin@live.cn
Organization name Stanford university
Department Genetics
Street address Stanford
City Palo Alto
State/province CA
ZIP/Postal code 94040
Country USA
 
Platforms (3)
GPL17769 Illumina MiSeq (synthetic construct)
GPL19424 Illumina NextSeq 500 (synthetic construct)
GPL23058 Illumina NextSeq 500 (Homo sapiens; synthetic construct)
Samples (12)
GSM5708114 Truncated ZNF140_F1-F6 construct replicate 1
GSM5708115 Truncated ZNF140_F1-F6 construct replicate 2
GSM5708116 Truncated ZNF10_F1-F8 construct replicate 1
Relations
BioProject PRJNA784587
SRA SRP348451

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
GSE189817_RAW.tar 910.0 Kb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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