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| Status |
Public on Oct 14, 2019 |
| Title |
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [HiC] |
| Organisms |
Drosophila melanogaster; Drosophila virilis; Drosophila busckii |
| Experiment type |
Other
Third-party reanalysis
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| Summary |
We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism.
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| Overall design |
This series includes data for Hi-C for D. melanogaster, D. busckii, and D. virilis and genome assembly for D. busckii and D. virilis. Genome assembly data are available at the foot of this record.
Previously published whole genome sequencing data were used in the assembly of the D. busckii contigs. Re-analyzed data includes PRJNA274996 (SRR1795010, SRR1794619, SRR1794616, SRR1794617, SRR1794614) and PRJNA196337 (SRR826809).
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| Contributor(s) |
Renschler G, Richard G, Valsecchi CI, Toscano S, Arrigoni L, Ramirez F, Akhtar A |
| Citation(s) |
31601616 |
| BioProject |
PRJNA450810 |
| |
| Submission date |
Oct 02, 2018 |
| Last update date |
Nov 25, 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
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| Lab |
Akhtar Lab
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| Platforms (4)
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| GPL23323 |
Illumina HiSeq 3000 (Drosophila melanogaster) |
| GPL25632 |
Illumina HiSeq 3000 (Drosophila busckii) |
| GPL25633 |
Illumina HiSeq 3000 (Drosophila virilis) |
| GPL25634 |
PacBio RS II (Drosophila busckii) |
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| Samples (5)
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| This SubSeries is part of SuperSeries: |
| GSE120752 |
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling |
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| Relations |
| SRA |
SRP140881 |
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