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Series GSE227552 Query DataSets for GSE227552
Status Public on May 29, 2024
Title NanoDam Profiling of EGL-43 and FOS-1 in Dopaminergic Neurons
Organism Caenorhabditis elegans
Experiment type Other
Summary Activity-dependent mechanisms have been long known to play a critical role in synaptogenesis. Here, we utilize a recently adapted technology, NanoDam, to perform targeted DamID using endogenously tagged GFP transcription factors.
 
Overall design A single copy insertion of a dopaminergic promoter driving expression of a GFP nanobody fused to Dam methylase was crossed together with animals carrying endogenous EGL-43::GFP and FOS-1::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
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Mar 16, 2023
Last update date May 29, 2024
Contact name Callista Yee
E-mail(s) calyee@stanford.edu
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 (9)
GSM7102586 L3 animals with dat-1_NanoDam control, replicate 1
GSM7102587 L3 animals with dat-1_NanoDam control, replicate 2
GSM7102588 L3 animals with dat-1_NanoDam control, replicate 3
This SubSeries is part of SuperSeries:
GSE260637 An activity regulated transcriptional program directly drives synaptogenesis
Relations
BioProject PRJNA945491

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
GSE227552_Dat-1_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.rep1.peaks.gff.gz 15.3 Kb (ftp)(http) GFF
GSE227552_Dat-1_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.rep2.peaks.gff.gz 14.8 Kb (ftp)(http) GFF
GSE227552_Dat-1_NanoDam_egl-43-vs-Dam.gatc-FDR0.01.rep3.peaks.gff.gz 13.2 Kb (ftp)(http) GFF
GSE227552_Dat-1_NanoDam_egl-43-vs-Dam.gatc.rep1.bedgraph.gz 3.1 Mb (ftp)(http) BEDGRAPH
GSE227552_Dat-1_NanoDam_egl-43-vs-Dam.gatc.rep2.bedgraph.gz 3.1 Mb (ftp)(http) BEDGRAPH
GSE227552_Dat-1_NanoDam_egl-43-vs-Dam.gatc.rep3.bedgraph.gz 1.9 Mb (ftp)(http) BEDGRAPH
GSE227552_Dat-1_NanoDam_egl-43_combined_1500.bed.gz 21.4 Kb (ftp)(http) BED
GSE227552_Dat-1_NanoDam_fos-1-vs-Dam.gatc-FDR0.01.rep1.peaks.gff.gz 14.4 Kb (ftp)(http) GFF
GSE227552_Dat-1_NanoDam_fos-1-vs-Dam.gatc-FDR0.01.rep2.peaks.gff.gz 14.3 Kb (ftp)(http) GFF
GSE227552_Dat-1_NanoDam_fos-1-vs-Dam.gatc-FDR0.01.rep3.peaks.gff.gz 12.3 Kb (ftp)(http) GFF
GSE227552_Dat-1_NanoDam_fos-1-vs-Dam.gatc.rep1.bedgraph.gz 2.5 Mb (ftp)(http) BEDGRAPH
GSE227552_Dat-1_NanoDam_fos-1-vs-Dam.gatc.rep2.bedgraph.gz 3.4 Mb (ftp)(http) BEDGRAPH
GSE227552_Dat-1_NanoDam_fos-1-vs-Dam.gatc.rep3.bedgraph.gz 1.4 Mb (ftp)(http) BEDGRAPH
GSE227552_Dat-1_NanoDam_fos-1_combined_1500.bed.gz 23.2 Kb (ftp)(http) BED
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Processed data are available on Series record

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