|
| Status |
Public on Nov 27, 2018 |
| Title |
HH30_PFL_WT_Hoxd10-11vp |
| Sample type |
SRA |
| |
|
| Source name |
Forelimb
|
| Organism |
Gallus gallus |
| Characteristics |
breed: White Leghorn
age: HH30
tissues: Proximal forelimb
genotype: wild type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The dissected limb bud tissues were dissociated with collagenase (Sigma Aldrich) and filtered through cell strainer to obtain single cells. Cells were fixed with 2% formaldehyde for 10 min at room temperature and the reaction was quenched on ice with glycine. Cells were further lysed with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 1x Protease inhibitor cocktail to isolate nuclei and stored at -80°C. Nuclei from pools of samples were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Sequences ligated to fragments of interest were digested again with DpnII (New England Biolabs), ligated with T4 DNA ligase HC (Promega) in diluted conditions.
These templates were amplified using Expand long template (Roche) and inversed PCR primers flanked with adaptors allowing multiplexing. All primer and barcode information are described in Supplemental Table 3 in Yakushiji-Kaminatsui et al. (2018).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
chick HH30 WT proximal forelimb Hoxd10-11 viewpoint
|
| Data processing |
Library strategy: 4C-Seq
De-multiplexing, mapping and 4C analysis were performed through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/). Reads were mapped to either the mm10 or galGal5 chicken genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters “--end-to-end --sensitive -k 20”. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads.
Fragments scores are normalized to the mean score of fragments falling into a region defined as the bait coordinated either ± 1Mb or ± 2Mb and the data was smoothed by using a running mean with window size of 11 fragments. During the procedure, information of excluded fragments at specific regions from the analysis were described in Supplemental Table 3 in Yakushiji-Kaminatsui et al. (2018).
Genome_build: mm10 or galGal5
Supplementary_files_format_and_content: Smoothed/normalized data (bedgraph)
|
| |
|
| Submission date |
Jun 11, 2018 |
| Last update date |
Nov 28, 2018 |
| Contact name |
Nayuta Yakushiji-Kaminatsui |
| E-mail(s) |
nayuta.yakushiji@riken.jp
|
| Phone |
+81 45 503 9690
|
| Organization name |
RIKEN Center for Integrative Medical Sciences
|
| Lab |
Laboratory for Developmental Genetics
|
| Street address |
1-7-22 Suehiro-cho, Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19005 |
| Series (2) |
| GSE115560 |
Similarities and differences in the regulation of HoxD genes during chick and mouse limb development [4C-seq] |
| GSE115563 |
Similarities and differences in the regulation of HoxD genes during chick and mouse limb development. |
|
| Relations |
| BioSample |
SAMN09390342 |
| SRA |
SRX4191477 |
