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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 [ChIP-seq] |
| Organisms |
Drosophila virilis; Drosophila busckii |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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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 |
We are submitting sex-seperated H4K16ac ChIP-seq datasets from D. busckii and D. virilis that were processed on our D. busckii and D. virilis genome assemblies that we are also providing here. For the H4K16ac ChIP-seq samples (2 replicates each) we provide histone 3 (H3) ChIP-seq samples (1 replicate for D. busckii, 2 replicates for D. virilis) as well as input samples (1 replicate for D. busckii, 2 replicates for D. virilis) as controls. We provide bigWig files of mapped reads of individual replicates as well as bigWig files of log2fold ratio input-normalized merged replicates. Processing of these samples was done on our D. busckii and D. virilis assemblies which we provide as fastq files. Raw data for generating both assemblies is deposited in SRA (SRR7029387-SRR7029398).
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| Contributor(s) |
Renschler G, Richard G, Valsecchi CI, Toscano S, Arrigoni L, Ramirez F, Akhtar A |
| Citation(s) |
31601616 |
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| Submission date |
Oct 02, 2018 |
| Last update date |
Nov 25, 2019 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
akhtarlab_data@ie-freiburg.mpg.de
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| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
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| Department |
Chromatin Regulation
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| Lab |
Akhtar Lab
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| Street address |
Stuebeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| Platforms (2) |
| GPL25632 |
Illumina HiSeq 3000 (Drosophila busckii) |
| GPL25633 |
Illumina HiSeq 3000 (Drosophila virilis) |
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| Samples (12)
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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 |
| BioProject |
PRJNA494470 |
| SRA |
SRP163268 |
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