high throughput sequencinginsecticide responseinsertions and deletionssingle nucleotide variantsGlobal climate change and acquired resistance to insecticides are threats to world food security. Drosophila suzukii, a devastating invasive pest in many parts of the world, causes substantial economic losses to ...
7c, d). Integrin receptors bind ECM components, suggesting that these proteins are also expressed within the nervous system. We thus tested expression of all genes annotated to encode proteins involved in extracellular matrix formation (FlyBase) using published single cell sequencing data of adult ...
Chromatin immunoprecipitation sequencing Tollrm9/Tollrm10 2-4-h-old embryos were collected for ChIP-seq and fixed as described above for Hi-C. Fixed embryos were flash frozen in liquid nitrogen and stored at −80 °C until further use. Frozen embryos were homogenized in sonication buffer ...
Sequencing was performed on two HiSeq X lanes. Genomes are available on NCBI with accession number: PRJNA669609. Gene annotations and determination of orthologs Nine draft assemblies deposited on NCBI genbank (D. albomicans, D. americana, D. montana, D. nasuta, D. pseudoobscura, D. robusta,...
Sequencing of library preparations was performed on Illumina Hiseq 4000 platform. Protein extraction for proteomic analysis Fly heads were homogenized by sonification for 5 min in urea lysis buffer (8 M urea, 1× proteinase inhibitor and phosphatase inhibitor (Roche), 2 mM EDTA). ...
Sequencing was performed on Illumina HiSeq 2500 according to the 10× Genomics V2 manual. For dataset1, ovaries from 200 flies were dissected and dissociated as described above to produce a single-cell solution. The solution of dissociated cells was subjected to MACS as described before32. ...
We thank Ina Nissen from the Quantitative Genomics Facility (QGF, D-BSSE, ETHZ) for preparing sequencing libraries and operating the GAIIx/HiSeq2000 sequencers. We thank Manuel Kohler (QGF and CISD, ETHZ) for managing next-generation sequencing data. We are grateful for computational resources ...
and loose pairing, consisting of single larger domains. Strikingly, active genomic regions (A-type compartments, active chromatin, expressed genes) correlated with tight pairing, suggesting that pairing has a functional implication genome-wide. Finally, using RNAi and haplotype-resolved Hi-C, we show...
After sequencing the vector, the transgenic fly lines were established by Bestgene Inc. To obtain the UAS-Rubicon::mRFP transgene, a Gateway entry vector (kind gift of Mari Suzuki, Tokyo Metropolitan Institute of Medical Science, Japan) bearing the full length Drosophila Rubicon cDNA coding ...
Biological duplicates of sequencing libraries were prepared from high quality RNA extracts (50 ng exRNA and 500 ng cellular RNA) using the Illumina TruSeq Stranded RNA Kit according to the manufacturer’s instructions. The TruSeq PE Clusterkit v3-cBot-HS was used on an Illumina HiSEq 2000...