title: Illumina 101 bp paired-end Hi-C library prepared from an asynchronous population of whole male pupae
design: In 2018, male pupae (Bradysia coprophila) were collected in the laboratory of Susan Gerbi (Brown University), flash frozen in bulk, and stored at -80*C. Briefly, for each batch, late larvae were picked from vials and placed on agar petri plates. Food and debris were removed from the larvae. The larvae were kept on the agar where they entered pupation asynchronously over 2-4 days. The mixed-stage pupae were collected in 2X SSC in an Eppendorf tube, centrifuged to remove the buffer, washed once with 1 ml 2X SSC and again centrifuged as much of the buffer removed as possible. The vial was then flash frozen in liquid nitrogen and stored at -80*C. Approximately 1000 pupae were collected across 11 tubes this way. Frozen pupae were shipped to Phase Genomics (Seattle, WA) on dry ice where they used the material as needed to prepare a Phase Genomics Proximo Hi-C sequencing library using the Proximo Hi-C 2.0 Kit, following the manufacturers protocols (https://info.phasegenomics.com/protocols). Briefly, the frozen male pupae were ground into a fine powder in two batches, and intact cells were crosslinked (formaldehyde), restriction digested (Sau3A1), end-repaired with biotinylated nucleotides, and proximity-ligated. Biotinylated molecules were pulled down with streptavidin beads and processed into an Illumina-compatible sequencing library, which was sequenced on an Illumina NovaSeq, generating a total of 115.2 million 2x101 bp paired end reads. This Hi-C data was used with Phase Genomics' Proximo Hi-C genome scaffolding platform to update the BU_Bcop_v1 (DDBJ/ENA/GenBank accession VSDI00000000 version VSDI01000000) assembly of the fungus gnat (Bradysia coprophila) genome to chromosome-scale scaffolds: BU_Bcop_v2 (DDBJ/ENA/GenBank accession VSDI00000000 version VSDI02000000). More information can be found here in the bioRxiv preprint, Chromosome-scale scaffolding of the fungus gnat genome (Diptera: Bradysia coprophila): https://www.biorxiv.org/content/10.1101/2022.11.03.515061v1 (DOI: 10.1101/2022.11.03.515061).