|
| Status |
Public on Jul 19, 2020 |
| Title |
RNAseq; whole fin; 2dpa; injured; batch 3; rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole fin
|
| Organism |
Danio rerio |
| Characteristics |
date: 2 dpa
tissue: whole fin
|
| Treatment protocol |
For fibroblast libraries, triplicate Tg(tph1b:creER;ubi:switch) caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen (Sigma-Aldritch) (Tornini et al., 2016). Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.
|
| Growth protocol |
D. rerio from the outbred Ekkwill (EK) strain ranging from 4 to 12 months were used for whole fin library preparations, Tg(tph1b:mCherry-NTR;ubi:switch) fish were used for fibroblast library preparation (Tornini et al 2016). Water temperature was maintained at 27.5°C, and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2-phenoxyethanol (Sigma-Aldrich) in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa, 1 dpa, or 4 dpa time points via razor blade (VWR) from 15 fish aged between 3-12 months. Fin tissue was collected in Tri-Reagent (Sigma) and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit-5 (Zymo).
RNA-seq libraries were prepared using a Stranded mRNA-seq Kit (KAPA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA-Seq reads were trimmed by Trim Galore (0.6.4, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq gene annotation).
Gene-level read counts were obtained using the htseq-count (v1.6.1) by the reads with MAPQ greater than 30.
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest for RNAseq
|
| |
|
| Submission date |
Apr 06, 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 |
| |
|
| Platform ID |
GPL21741 |
| Series (1) |
| GSE146960 |
Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins |
|
| Relations |
| BioSample |
SAMN14544114 |
| SRA |
SRX8062811 |
