|
| Status |
Public on Feb 16, 2023 |
| Title |
whole body discarding last third from the cloaca, 15dph, rep1 [ATAC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
whole body discarding last third from the cloaca
|
| Organism |
Scophthalmus maximus |
| Characteristics |
tissue: whole body discarding last third from the cloaca
developmental stage: 15 days post hatching
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Turbots at different stages were collected to reach 75,000 cells per sample. 3dpf stage was treated with 1mg/ml pronase in 1X PBS to remove the chorion. Cells were lysated after incubation with 10mM Tris, 10mM NaCl, 3mM MgCl2, 0.1% NP40 for transposition reaction and PCR amplification.
Transposition with Tn5 enzyme and PCR amplification
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
15_idrConsPeaks.bed
|
| Data processing |
Alignment of reads with Bowtiew2
Duplicated removal and correction of start position with Bedtools
Peak calling with MACS2 and IDR algorithm
Assembly: Turbot genome: http://ftp.ensembl.org/pub/release-107/fasta/scophthalmus_maximus/dna/
Supplementary files format and content: IDR peaks in BED format
Supplementary files format and content: bigWig format for displaying in a genome browser track
|
| |
|
| Submission date |
Oct 13, 2022 |
| Last update date |
Feb 22, 2023 |
| Contact name |
Laura Guerrero Peña |
| E-mail(s) |
lguerrero@iim.csic.es
|
| Phone |
+34 986231930
|
| Organization name |
CSIC
|
| Department |
Aquaculture and Biotecnology
|
| Lab |
Rotllant's Lab
|
| Street address |
Eduardo Cabello, 8
|
| City |
Vigo |
| State/province |
Pontevedra |
| ZIP/Postal code |
36208 |
| Country |
Spain |
| |
|
| Platform ID |
GPL32742 |
| Series (2) |
| GSE215396 |
Chromatin accessibility at four key stages of turbot development, from phylotypic to post-metamorphic stages [ATAC-seq] |
| GSE215397 |
Genome-wide chromatin accessibility and gene expression profiling during flatfish metamorphosis |
|
| Relations |
| BioSample |
SAMN31269623 |
| SRA |
SRX17877714 |
