|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on May 29, 2024 |
Title |
ATAC-seq Profiling of Mixed Stage C. elegans Neuronal Nuclei |
Organism |
Caenorhabditis elegans |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
Summary |
Using ATAC-seq, we aimed to identify regions of open chromatin in the developing C. elegans nervous system. This dataset was used to determine regions of chromatin and compare it to ChIP-seq data of TFs of interest, to assist us in identifying ChIP-seq peaks which are solely expressed in neurons (vs. general, total worm binding). Specifically, since EGL-43 is expressed in many tissues, including both neuronal and the somatic gonad, ATAC-seq was particularly helpful in identifying neuronal-specific ChIP-seq peaks and NanoDam peaks of interest (GSE227552).
|
|
|
Overall design |
We utilized a strongly expressed pan-neuronal nuclear GFP strain, and grew worms to density as a mixed stage population, with the majority being larval animals. Then, we used standard homogenizing procedures using a stainless steel dounce and ChIP-seq buffers to isolate neuronal nuclei. Nuclei were sorted on a FACSAria Fusion with DAPI to stain for nuclei. Neuronal nuclei were gated as GFP+ and DAPI+; Total Nuclei were gated as DAPI+, and 50,000 nuclei were used for each sample. Nuclei were subjected immediately to Tn5 transposition and amplification.
|
|
|
Contributor(s) |
Yee C, Shen K |
Citation(s) |
39103556 |
|
Submission date |
Feb 29, 2024 |
Last update date |
Sep 09, 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) |
GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
|
Samples (6)
|
GSM8121367 |
Mixed stage neuronal nuclei, replicate 1 |
GSM8121368 |
Mixed stage neuronal nuclei, replicate 2 |
GSM8121369 |
Mixed stage neuronal nuclei, replicate 3 |
|
This SubSeries is part of SuperSeries: |
GSE260637 |
An activity regulated transcriptional program directly drives synaptogenesis |
|
Relations |
BioProject |
PRJNA1082385 |
Supplementary file |
Size |
Download |
File type/resource |
GSE260636_Neuronal_ppr.IDR0.1.narrowPeak.gz |
60.8 Kb |
(ftp)(http) |
NARROWPEAK |
GSE260636_Total_ppr.IDR0.1.narrowPeak.gz |
69.5 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|