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Series GSE232946 Query DataSets for GSE232946
Status Public on Jun 30, 2023
Title NanoDam Profiling of EGL-43 in the Anchor Cell
Organism Caenorhabditis elegans
Experiment type Other
Summary Depending on the cellular context, TF expression can vary dramatically both spatially and temporally. These differences in expression patterns can result in tissue-specific differences in TF binding to downstream targets. To identify targets on a tissue-specific basis, Targeted DamID (TaDa) has been recently introduced to generate TF binding profiles in various models including C. elegans. However, TaDa suffers from portability such that a new promoter-TF fusion transgene must be constructed for every new experimental condition of interest. Here, we adapt NanoDam for usage in C. elegans, which relies on the use of endogenous TF-GFP knock-ins, a plethora of which have already been generated by the community. We report that NanoDam single copy transgenes consisting of lowly expressed, tissue-specific GFP nanobody-Dam fusions, when combined with endogenous GFP-tagged alleles of TFs, results in robust, tissue-specific profiling. Using an endogenous GFP-tagged allele of EGL-43/EVI1, we performed NanoDam profiling of two disparate tissue types, the anchor cell (AC) and dopaminergic neurons, and identify targets unique to each and shared by both cell types. We also identify two GATA TFs, ELT-6 and EGL-18, as novel regulators of AC invasion. Taken together, we demonstrate that NanoDam is capable of profiling endogenous GFP-tagged TFs to identify novel downstream targets in specific cell types of C. elegans.
Overall design A single copy insertion of an Anchor Cell promoter driving expression of a GFP nanobody fused to Dam methylase was crossed together with animals carrying endogenous EGL-43::GFP. Dam methylase permanently methylated DNA in close proximity to regions of TF binding. DNA from L3 worms was extracted, digested with DpnI, amplified, and sequenced using the MinION Nanopore platform
Contributor(s) Yee C, Shen K
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Submission date May 19, 2023
Last update date Jun 30, 2023
Contact name Callista Yee
Organization name Stanford University/HHMI
Street address 327 Campus Drive, Shen lab, Bass Biology 329
City Stanford
State/province California
ZIP/Postal code 94305
Country USA
Platforms (1)
GPL26522 MinION (Caenorhabditis elegans)
Samples (6)
GSM7397962 L3 animals with lin-29_NanoDam control, replicate 1
GSM7397963 L3 animals with lin-29_NanoDam control, replicate 2
GSM7397964 L3 animals with lin-29_NanoDam control, replicate 3
BioProject PRJNA974461

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

Supplementary file Size Download File type/resource
GSE232946_lin-29_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.peaks.rep1.gff.gz 16.9 Kb (ftp)(http) GFF
GSE232946_lin-29_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.peaks.rep2.gff.gz 16.0 Kb (ftp)(http) GFF
GSE232946_lin-29_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.peaks.rep3.gff.gz 17.1 Kb (ftp)(http) GFF
GSE232946_lin-29_NanoDam_egl-43-vs-Dam.gatc.rep1.bedgraph.gz 3.4 Mb (ftp)(http) BEDGRAPH
GSE232946_lin-29_NanoDam_egl-43-vs-Dam.gatc.rep2.bedgraph.gz 3.1 Mb (ftp)(http) BEDGRAPH
GSE232946_lin-29_NanoDam_egl-43-vs-Dam.gatc.rep3.bedgraph.gz 3.3 Mb (ftp)(http) BEDGRAPH
GSE232946_lin-29_NanoDam_egl-43_combined_1500.bed.gz 37.9 Kb (ftp)(http) BED
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