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| Status |
Public on Jul 19, 2020 |
| Title |
ATACseq; Fibroblast; 4dpa; injured; batch 3; rep1 |
| Sample type |
SRA |
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| Source name |
ATACseq; Fibroblast; 4dpi; injured
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| Organism |
Danio rerio |
| Characteristics |
time: 4 dpa
tissue: fibroblast
genotype: wild type
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| 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.
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| 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), and homozygous evx1 knockout fish were used for evx1 libraries (Schulte et al 2011). 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.
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| Extracted molecule |
genomic DNA |
| 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. Homozygous evx1 knockout fish were used for evx1 knockout libraries. 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).
For ATAC-seq libraries, 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 3-12 months. Homozygous Evx1 knockout fish (screened visually by jointless phenotype) (Borday et al., 2001) were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH (Roche) in Hank’s Balanced Salt Solution (Gibco) stirring at 37°C for 2 hours, collected in 15 minute increments, then strained through a 70 μm nylon cell strainer (Corning). Samples were quantitated for 100K live cells using the Countess Automated Cell Counter (Thermo Fisher Scientific).Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B-C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter.
RNA-seq libraries were prepared using a Stranded mRNA-seq Kit (KAPA).
ATAC-seq library preparation was performed as detailed in (Buenrostro et al., 2013).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| 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.
ATAC-Seq reads were trimmed by Trim Galore (0.4.1, with -q 15) and then mapped with bowtie2(2.2.5, with parameters --very-sensitive) to zebrafish genome (UCSC danRer10 refSeq annotation).
The mapped reads were filtered by MAPQ greater than 30 by samtools (v 1.5) and duplicated reads were removed by picard (v 1.91). Bigwig files were generated by kentUtils.
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph
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| Submission date |
Mar 13, 2020 |
| Last update date |
Jan 10, 2023 |
| Contact name |
jianhong ou |
| E-mail(s) |
jianhong.ou@duke.edu
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| Phone |
5084102796
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| Organization name |
Duke University
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| Department |
Cell Biology
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| Lab |
Regeneromics
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| Street address |
465 Nanaline Duke Building, Duke University Medical Center
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| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27710 |
| Country |
USA |
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| Platform ID |
GPL21741 |
| Series (1) |
| GSE146960 |
Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins |
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| Relations |
| BioSample |
SAMN14375545 |
| SRA |
SRX7910581 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4411441_Fibro_injured.rep1.bw |
215.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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