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Series GSE260636 Query DataSets for GSE260636
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

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SOFT formatted family file(s) SOFTHelp
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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
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Raw data are available in SRA
Processed data are available on Series record

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