|
| Status |
Public on Dec 16, 2015 |
| Title |
Amphioxus_15hpf (4) |
| Sample type |
SRA |
| |
|
| Source name |
15hpf amphioxus embryos
|
| Organism |
Branchiostoma lanceolatum |
| Characteristics |
age: 15hpf
tissue: whole embryos
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Embryos were obtained and raised as previously described (Fuentes et al 2007 J Exp Zoolog B Mol Dev Evol 308:484–493)
|
| 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 |
European amphioxus
|
| Data processing |
library strategy: 4C-Seq
For 4C: Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the danRer7 assembly and Sc_hox scaffold 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. Reads located in fragments flanked by two restriction sites of the same enzyme, or in fragments smaller than 40 bp were filtered out
Mapped reads were then converted to reads-per-first-enzyme-fragment-end units, and smoothed using a 30 DpnII fragments mean running window algorithm.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: danRer7/Sc_hox (see Sc_hox fasta linked as supplementary file on Series record)
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 4Cseq of viewpoint that can be directly uploaded to UCSC for visualization.
For ATAC-seq: Alignment: reads were aligned using Sc_hox scaffold as reference genome and Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using local browser
Genome_build: Sc_hox (see Sc_hox fasta linked as supplementary file on Series record)
Supplementary_files_format_and_content: bigWig format for visualization
|
| |
|
| Submission date |
May 11, 2015 |
| Last update date |
May 15, 2019 |
| 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 |
GPL20177 |
| Series (1) |
| GSE68737 |
A single 3D chromatin compartment in amphioxus Hox cluster suggests a stepwise evolutionary origin for vertebrate Hox bimodal regulatory topologies |
|
| Relations |
| BioSample |
SAMN03652063 |
| SRA |
SRX1023182 |
