|
| Status |
Public on Oct 14, 2019 |
| Title |
Dbus_Hi-C_for_assembly |
| Sample type |
SRA |
| |
|
| Source name |
fly embryos
|
| Organism |
Drosophila busckii |
| Characteristics |
strain: San Diego stock center, stock number 13000-0081.31
developmental stage: late stage 16 embryos
tissue: embryos
|
| Growth protocol |
D. melanogaster and D. virilis flies were maintained in standard Drosophila medium. D. busckii flies were additionally fed with instant Drosophila medium (Formula 4-24, Carolina Biological Supply Company, catalog number 173202) mixed with instant potato powder on top of the standard Drosophila medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
In situ Hi-C experiments were performed using a modified version of the in situ Hi-C protocol (Rao et al. 2014) described in (Ramirez et al. 2018). Nuclei were extracted by resuspension in 1 mL ice-cold lysis buffer (10 mM Tris-HCl, pH 8, 10 mM NaCl, 0.2% IGEPAL CA-630) and sonication following the standardized nuclear extraction NEXON protocol (Arrigoni et al. 2015) (Covaris E220 sonicator, settings: 75 W peak power, 2 % duty factor, 200 cycles/burst, for 15-30 sec until about 70 % of intact nuclei were released). Samples were filtered through a 30 µm filter to remove bigger embryo fragments. From this step on we followed the protocol described in (Ramirez et al. 2018). Nuclei were digested using DpnII (NEB, R0543M, 150 U/ sample).
NEB Next Ultra II
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
We used our Hi-C data and PacBio data (SRR7029398, SRR7029397) in combination with published whole genome sequencing reads ((Zhou and Bachtrog 2015) and (Vicoso and Bachtrog 2015) accession codes SRR1795010, SRR1794619, SRR1794616, SRR1794617, SRR1794614 and SRR826809) for de novo genome assembly.
Genome assembly and hard-masked genome assembly of D. busckii
|
| Data processing |
Hi-C: Paired-end reads were mapped using bwa mem with parameters -A1 -B4 -E50 -L0 (which promote a read to be split instead of adding a gap) and Hi-C matrices generated using `hicBuildMatrix`, Hi-C matrices of replicates were merged using `hicSumMatrices` and corrected at restriction enzyme resolution using `hicCorrectMatrix` tools from HiCExplorer v1.8.1. TAD boundaries were called using the `hicFindTADs` tool from HiCExplorer with settings `--minDepth 15000 --maxDepth 50000 --step 2000 --thresholdComparisons 0.01 --correctForMultipleTesting bonferroni`.
Supplementary_files_format_and_content: FASTA files of the D.busckii assembly are available on the series record.
|
| |
|
| Submission date |
Oct 02, 2018 |
| Last update date |
Oct 14, 2019 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
akhtarlab_data@ie-freiburg.mpg.de
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Chromatin Regulation
|
| Lab |
Akhtar Lab
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25632 |
| Series (2) |
| GSE120751 |
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [HiC] |
| GSE120752 |
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling |
|
| Relations |
| BioSample |
SAMN08947965 |
| SRA |
SRX3961620 |
