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Status |
Public on Dec 15, 2021 |
Title |
Spec-seq data for ZNF140, ZNF10, ZFP3, ZNF675, ZNF382 |
Organisms |
Homo sapiens; synthetic construct |
Experiment type |
Other
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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.
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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.
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Contributor(s) |
Zuo Z |
Citation(s) |
37680368 |
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Submission date |
Nov 29, 2021 |
Last update date |
Oct 02, 2023 |
Contact name |
Zheng Zuo |
E-mail(s) |
zeropin@live.cn
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Organization name |
Stanford university
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Department |
Genetics
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Street address |
Stanford
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City |
Palo Alto |
State/province |
CA |
ZIP/Postal code |
94040 |
Country |
USA |
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Platforms (3) |
GPL17769 |
Illumina MiSeq (synthetic construct) |
GPL19424 |
Illumina NextSeq 500 (synthetic construct) |
GPL23058 |
Illumina NextSeq 500 (Homo sapiens; synthetic construct) |
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Samples (12)
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GSM5708114 |
Truncated ZNF140_F1-F6 construct replicate 1 |
GSM5708115 |
Truncated ZNF140_F1-F6 construct replicate 2 |
GSM5708116 |
Truncated ZNF10_F1-F8 construct replicate 1 |
GSM5708117 |
Truncated ZNF10_F1-F8 construct replicate 2 |
GSM5708118 |
Truncated ZFP3_F1-F10 construct replicate 1 |
GSM5708119 |
Truncated ZFP3_F1-F10 construct replicate 2 |
GSM5708120 |
ZNF675_F1-F11 construct replicate 1 |
GSM5708121 |
ZNF675_F1-F11 construct replicate 2 |
GSM5708122 |
Truncated ZNF675_F1-F6 construct replicate 1 |
GSM5708123 |
Truncated ZNF675_F1-F6 construct replicate 2 |
GSM6632802 |
ZNF382 construct replicate 1 |
GSM6632803 |
ZNF382 construct replicate 2 |
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Relations |
BioProject |
PRJNA784587 |
SRA |
SRP348451 |