|
| Status |
Public on Jan 12, 2023 |
| Title |
HiC Skate st30 Pectoral fin replicate 2b |
| Sample type |
SRA |
| |
|
| Source name |
Pectoral fin
|
| Organism |
Leucoraja erinaceus |
| Characteristics |
developmental timing: stage 30
treatment: Control
|
| Growth protocol |
Embryos were kept at 15 °C in reconstituted Instant Ocean (Aquarium systems) with 12 h light–dark cycles.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryonic skate fin buds were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lyses and extracted nuclei were processed for in-situ HiC preparation as previously described (Rao et al. 2014). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. DNA was extracted after cross-link reversal and sonicated in a Covaris M220 sonicator for fragments between 150-600 bp. Proximity ligation products were enriched using Streptavidin-coated beads.
End-repair, A-tailing and ligation of indexing adapters followed standard procedure for Illumina library preparations for paired-end sequencing. Final library was prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
HiC_Skate30_Pectoral_rep2.hic
|
| Data processing |
Reads from technical replicates were pooled and aligned using BWA Ligation events were detected using Pairtools and filtered for non-ligated and self-ligated events Ligation events were detected using Pairtools and filtered for non-ligated and self-ligated events
Binary multiresolution hic files were generated using Juicer Tools Pre
Genome_build: custom assembly (uploaded in the same Bioproject)
Supplementary_files_format_and_content: hic format
|
| |
|
| Submission date |
Nov 16, 2021 |
| Last update date |
Jan 12, 2023 |
| Contact name |
Juan J. Tena |
| E-mail(s) |
jjtenagu@upo.es
|
| Organization name |
CABD/CSIC
|
| Street address |
Univ. Pablo Olavide, Ctra. Utrera km1
|
| City |
Sevilla |
| ZIP/Postal code |
41013 |
| Country |
Spain |
| |
|
| Platform ID |
GPL30966 |
| Series (2) |
| GSE188979 |
The little skate genome and the evolutionary emergence of wing-like fin appendages [Hi-C] |
| GSE188980 |
The little skate genome and the evolutionary emergence of wing-like fin appendages |
|
| Relations |
| BioSample |
SAMN23217785 |
| SRA |
SRX13151034 |
