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Series GSE146960 Query DataSets for GSE146960
Status Public on Jul 19, 2020
Title Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Mammalian genomes likely encode all gene products required to regenerate an amputated limb, yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non-mammalian vertebrates possess these instructions, which exist as gene cis-regulatory elements. Here, to identify candidate tissue regeneration enhancer elements (TREEs) important for zebrafish fin regeneration, we performed ATAC-seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration, and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs, we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes, including fgf20a, cx43, and mdka, with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis-regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration.
 
Overall design Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa, and fibroblast 0 dpa and fibroblast 4 dpa.
 
Contributor(s) Thompson JD, Ou J, Poss KD
Citation(s) 32665240
Submission date Mar 13, 2020
Last update date Jan 10, 2023
Contact name jianhong ou
E-mail(s) jianhong.ou@duke.edu
Phone 5084102796
Organization name Duke University
Department Cell Biology
Lab Regeneromics
Street address 465 Nanaline Duke Building, Duke University Medical Center
City Durham
State/province North Carolina
ZIP/Postal code 27710
Country USA
 
Platforms (1)
GPL21741 Illumina HiSeq 4000 (Danio rerio)
Samples (36)
GSM4411406 RNAseq; whole fin; 0dpa; uninjured; batch 1; rep1
GSM4411407 RNAseq; whole fin; 0dpa; uninjured; batch 1; rep2
GSM4411408 RNAseq; whole fin; 4dpa; injured; batch 1; rep1
Relations
BioProject PRJNA612515
SRA SRP252754

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE146960_RAW.tar 4.2 Gb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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