|
| Status |
Public on Jan 12, 2023 |
| Title |
HiChIP H3K4me3 Skate st31 Pectoral Anterior fin replicate 1b |
| Sample type |
SRA |
| |
|
| Source name |
Pectoral anterior fin
|
| Organism |
Leucoraja erinaceus |
| Characteristics |
developmental timing: stage 31
treatment: Control
antibody: H3K4me3
|
| 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 |
Either anterior or posterior portions of skate embryonic find buds were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lysed and extracted nuclei were processed for HiChIP preparation as previously described (Mumbach et al. 2016). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. Chromatin was sonicated in a Covaris M220 sonicator for fragments around 300 bp and immunoprecipitated with anti-H3K4me3 (abcam). DNA was extracted after cross-link reversal and biotinylated products were recovered with streptavidin-coated beads, TAGmented with Tn5 transposase and purified for library preparation.
Preparation of HiChIP libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
HiChIP_H3K4me3_Skate31_Pectoral_Ant.hic
|
| Data processing |
Library strategy: HiChIP
Reads from biological replicates were pooled and aligned using GEM Ligation events were detected using TADbit 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) |
| GSE188976 |
The little skate genome and the evolutionary emergence of wing-like fin appendages [HiChIP] |
| GSE188980 |
The little skate genome and the evolutionary emergence of wing-like fin appendages |
|
| Relations |
| BioSample |
SAMN23216799 |
| SRA |
SRX13151029 |
