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| Status |
Public on May 29, 2024 |
| Title |
NanoDam Profiling of EGL-43 and FOS-1 in Dopaminergic Neurons |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Other
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| 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.
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| 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
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| Contributor(s) |
Yee C, Shen K |
| Citation(s) |
39103556 |
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| Submission date |
Mar 16, 2023 |
| Last update date |
Sep 09, 2024 |
| Contact name |
Callista Yee |
| E-mail(s) |
calyee@stanford.edu
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| Organization name |
Stanford University/HHMI
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| Street address |
327 Campus Drive, Shen lab, Bass Biology 329
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL26522 |
MinION (Caenorhabditis elegans) |
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| Samples (9)
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| 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 |
| GSM7102589 |
L3 animals with dat-1 NanoDam and EGL-43::GFP, replicate 1 |
| GSM7102590 |
L3 animals with dat-1 NanoDam and EGL-43::GFP, replicate 2 |
| GSM7102591 |
L3 animals with dat-1 NanoDam and EGL-43::GFP, replicate 3 |
| GSM7102592 |
L3 animals with dat-1 NanoDam and FOS-1::GFP, replicate 1 |
| GSM7102593 |
L3 animals with dat-1 NanoDam and FOS-1::GFP, replicate 2 |
| GSM7102594 |
L3 animals with dat-1 NanoDam and FOS-1::GFP, replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE260637 |
An activity regulated transcriptional program directly drives synaptogenesis |
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| Relations |
| BioProject |
PRJNA945491 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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