Comment[ArrayExpressAccession] E-MTAB-8877 Comment[Submitted Name] Whole genome sequencing of a panel of genetically diverse crosses of Drosophila melanogaster Investigation Title Whole genome sequencing of a panel of genetically diverse crosses of Drosophila melanogaster Experiment Description Whole genome sequencing of 8 F1 Drosophila lines along with the two parental lines for one of the F1 genotypes. Data were sequenced to verify previously published genome sequences (parental lines: DGRP, maternal line: PMID31308546) and to identify potentially unbalanced SNPs within the data that might confound allele-specific measurements in the F1 lines. Experimental Design strain or line design Experimental Design Term Source REF EFO Quality Control Type Quality Control Term Source REF Experimental Factor Name strain Experimental Factor Type strain Person Last Name Girardot Garfield Zhao Floc'hlay Person First Name Charles David Bingqing Swann Person Email Charles.Girardot@embl.de dagarfield@gmail.com bingqing.zhao@gmail.com flochlay@biologie.ens.fr Person Affiliation European Molecular Biology Laboratory European Molecular Biology Laboratory European Molecular Biology Laboratory Ecole National Superieure Person Roles submitter investigator;data analyst investigator investigator;data analyst Public Release Date 2021-02-25 Protocol Name P-MTAB-94373 P-MTAB-94374 P-MTAB-94375 P-MTAB-94376 Protocol Type sequencing nucleic acid library construction protocol growth protocol nucleic acid extraction protocol Protocol Description Standard NextSeq500 Single End Sequencing The resulting gDNA was processed into a sequencing library using Illumina NextSeq 75bp SE. The virginizer flies of 5-10 days age were transferred into fresh bottles and left to lay embryos for about 24 hours at 20C before the adults were removed from the bottles. The bottles were heat-shocked inside a 38C water bath for 1 hour. The virgins eclosed from heat-shocked bottles of the virginizer line were collected, mated to the hand-picked males from the paternal lines by putting all flies into cylindrical fly houses in a 25C room. The flies were left in the cages for 2 days before starting the collections. On the day of collection, one hour prelays were done for 3 times, followed by 2-hour collections. The plates with embryos were aged to the stages desired at 25C. The embryos were washed onto the set of sieves and dechorionated by incubating in the 50% bleach for 2.5 min. Around 200 embryos were transferred into an eppendorf tube and snap-frozen in liquid nitrogen for RNA assays. The majority of embryos were fixed by incubating in 9.5 ml cross-linking solution with 485 microliters 37% formadehyde with vigorous shaking for 15 min. Cross-linking was stopped by incubating with Glycine solution with vigorous shaking for at least 1 min. After washing with PBT, the embryos were blotted dry. The cross-linked dry embryos were transferred into 1.5 mL eppendorf tubes, snap-frozen in liquid nitrogen and kept in -80C for ATAC-seq and iChiP. We isolated gDNA from ~100 embryos per F1 cross using an electric pestle and Solution A from Qiagen (0.1mM Tris-HCl pH9.0 / 0.1 M EDTA / 1% SDS). Following this step, the lysate was incubated for 30 min at 65C followed by the addition of 28 microl 8M KAc and 30min incubation on ice. The debris was then spun down and the supernatant cleaned up using a standard Phenol/Chloroform extraction. Protocol Hardware NextSeq 500 Protocol Term Source REF EFO EFO EFO EFO Term Source Name MGED Ontology ArrayExpress EFO Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/ Comment[AEExperimentType] DNA-seq Comment[SecondaryAccession] ERP120379 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/ERR3975588-ERR3975595 SDRF File E-MTAB-8877.sdrf.txt