|
| Status |
Public on Mar 23, 2021 |
| Title |
Otx_braLan_15hpf_4C-seq |
| Sample type |
SRA |
| |
|
| Source name |
15 hpf amphioxus embryos
|
| Organism |
Branchiostoma lanceolatum |
| Characteristics |
4c-seq bait: Otx promoter
tissue: whole embryos
Stage: 15 hpf
|
| Growth protocol |
Embryos were cultivated at 19°C in filtered seawater until desired developmental stage
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
4C-seq experiments performed using as bait the specified promoter
|
| Data processing |
Library strategy: 4C-Seq
Demultiplexing: Different samples were demultiplexed using the primer sequences
Mapping: Reads were mapped to the Branchiostoma lanceolatum (Bl71nemr assembly) or Danio rerio (danRer7 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: Only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
Data visualization: Data were uploaded to UCSC Browser for visualization.
Genome_build: danRer7/Bl71nemr(http://amphiencode.github.io/Data/)
Supplementary_files_format_and_content: BEDGRAPH
|
| |
|
| Submission date |
Aug 28, 2019 |
| Last update date |
Mar 24, 2021 |
| Contact name |
Rafael Domínguez Acemel |
| E-mail(s) |
rdacemel@gmail.com
|
| Organization name |
Max Delbrück Center for Molecular Medicine (MDC)
|
| Department |
Berlin Institute of Medical Systems Biology (BIMSB)
|
| Lab |
AG Lupiañez
|
| Street address |
Hannoversche Str. 28
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20177 |
| Series (1) |
| GSE136554 |
Ancient genomic regulatory blocks are a major source for gene deserts in vertebrates after whole genome duplications |
|
| Relations |
| BioSample |
SAMN12647463 |
| SRA |
SRX6780711 |
