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| Status |
Public on Feb 16, 2023 |
| Title |
Chromatin accessibility at four key stages of turbot development, from phylotypic to post-metamorphic stages [ATAC-seq] |
| Organism |
Scophthalmus maximus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Metamorphosis is a widely studied post-embryonic process in which many tissues undergo dramatic modifications to adapt to the new adult lifestyle. Flatfish represent a good example of metamorphosis in teleosts. During flatfish metamorphosis, organ regression and neo-formation occur, being the most remarkable change the migration of one of the eyes to the other side of the body. In order to create a useful and reliable tool to advance the molecular study of metamorphosis in flatfish, we generated a chromatin accessible atlas as well as gene expression profile during four developmental stages ranging from a phylotypic stage to a post-metamorphic stage. We identified 29,019 accessible regions of chromatin and 3,253 differentially expressed genes. We found stage-specific regulatory regions and gene expression profile, supporting the quality of the results. Our work provides strongly reproducible data for further studies to elucidate the regulatory elements that ensure successful metamorphosis.
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| Overall design |
ATACseq experiments in different developmental stages in Scophthalmus maximus
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| Contributor(s) |
Guerrero-Peña L, Suarez-Bregua P, Gil-Gálvez A, Naranjo S, Méndez-Martínez L, Tur R, García-Fernández P, Tena JJ, Rotllant J |
| Citation(s) |
37031231 |
| Submission date |
Oct 13, 2022 |
| Last update date |
May 03, 2023 |
| Contact name |
Laura Guerrero Peña |
| E-mail(s) |
lguerrero@iim.csic.es
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| Phone |
+34 986231930
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| Organization name |
CSIC
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| Department |
Aquaculture and Biotecnology
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| Lab |
Rotllant's Lab
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| Street address |
Eduardo Cabello, 8
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| City |
Vigo |
| State/province |
Pontevedra |
| ZIP/Postal code |
36208 |
| Country |
Spain |
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| Platforms (1) |
| GPL32742 |
Illumina HiSeq 2500 (Scophthalmus maximus) |
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| Samples (8)
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| GSM6634798 |
whole, 3dpf, rep1 [ATAC-seq] |
| GSM6634799 |
whole, 3dpf, rep2 [ATAC-seq] |
| GSM6634800 |
whole body discarding last third from the cloaca, 15dph, rep1 [ATAC-seq] |
| GSM6634801 |
whole body discarding last third from the cloaca, 15dph, rep2 [ATAC-seq] |
| GSM6634802 |
whole body discarding last third from the cloaca, 23dph, rep1 [ATAC-seq] |
| GSM6634803 |
whole body discarding last third from the cloaca, 23dph, rep2 [ATAC-seq] |
| GSM6634804 |
whole body discarding last third from the cloaca, 37dph, rep1 [ATAC-seq] |
| GSM6634805 |
whole body discarding last third from the cloaca, 37dph, rep2 [ATAC-seq] |
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| This SubSeries is part of SuperSeries: |
| GSE215397 |
Genome-wide chromatin accessibility and gene expression profiling during flatfish metamorphosis |
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| Relations |
| BioProject |
PRJNA890207 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE215396_15_idrConsPeaks.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSE215396_21_idrConsPeaks.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE215396_37_idrConsPeaks.bed.gz |
1.1 Mb |
(ftp)(http) |
BED |
| GSE215396_3_idrConsPeaks.bed.gz |
2.3 Mb |
(ftp)(http) |
BED |
| GSE215396_RAW.tar |
686.3 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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