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| Status |
Public on Jan 12, 2023 |
| Title |
The little skate genome and the evolutionary emergence of wing-like fin appendages [ATAC-seq] |
| Organism |
Leucoraja erinaceus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
While retaining ancestral morphological and genomic traits, skates evolved a novel body plan with remarkably enlarged wing-like fins that allowed skates to thrive in benthic environments, but their molecular underpinnings remain elusive. Here we investigate the origin of this phenotypical innovation by assembling a high-quality chromosome-scale genome sequence for the little skate Leucoraja erinacea and by generating extensive regulatory profiling datasets in developing fins (gene expression, chromatin occupancy and conformation). We show that despite their derived morphology, the skate genome retains multiple features of the ancestral jawed vertebrate genome.
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| Overall design |
ATACseq, RNAseq, HiC and HiChIP experiments in skate fins samples
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| Contributor(s) |
Marlétaz F, de la Calle-Mustienes E, Acemel RD, Nakamura T, Paliou C, Naranjo S, Martínez-García PM, Cases I, Sleight V, Hirschberger C, Andrescavage A, Marcet-Houben M, Bogdanovic O, Yang L, Gallardo-Fuentes L, Sospedra I, Lopez-Rios J, Darbellay F, Visel A, Dekker J, Shubin N, Gillis JA, Gabaldón T, Tena JJ, Lupianez D, Rokhsar DS, Gómez-Skarmeta JL |
| Citation(s) |
37046085 |
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| Submission date |
Nov 16, 2021 |
| Last update date |
Apr 14, 2023 |
| Contact name |
Juan J. Tena |
| E-mail(s) |
jjtenagu@upo.es
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| Organization name |
CABD/CSIC
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| Street address |
Univ. Pablo Olavide, Ctra. Utrera km1
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| City |
Sevilla |
| ZIP/Postal code |
41013 |
| Country |
Spain |
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| Platforms (1) |
| GPL30966 |
DNBSEQ-G400 (Leucoraja erinacea) |
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| Samples (8)
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| GSM5692711 |
ATACseq Skate st31 Pectoral Anterior fin replicate 1 |
| GSM5692712 |
ATACseq Skate st31 Pectoral Anterior fin replicate 2 |
| GSM5692713 |
ATACseq Skate st31 Pectoral Posterior fin replicate 1 |
| GSM5692714 |
ATACseq Skate st31 Pectoral Posterior fin replicate 2 |
| GSM5692715 |
ATACseq Skate st31 Pelvic fin replicate 1 |
| GSM5692716 |
ATACseq Skate st31 Pelvic fin replicate 2 |
| GSM5692717 |
ATACseq Skate st31 Pelvic fin replicate 3 |
| GSM5692718 |
ATACseq Skate st31 Pelvic fin replicate 4 |
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| This SubSeries is part of SuperSeries: |
| GSE188980 |
The little skate genome and the evolutionary emergence of wing-like fin appendages |
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| Relations |
| BioProject |
PRJNA780926 |
| SRA |
SRP346406 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE188972_RAW.tar |
2.9 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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