title: Cis_reg_DNA_852
organism: Drosophila melanogaster
description: Protocols: 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. The resulting gDNA was processed into a sequencing library using Illumina NextSeq 75bp SE.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-12-04T04:07:44Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2020-03-05T11:23:16Z
attributes.tag: External Id
attributes.value: SAMEA6604964
attributes.tag: INSDC center name
attributes.value: EMBL
attributes.tag: INSDC first public
attributes.value: 2020-12-04T04:07:44Z
attributes.tag: INSDC last update
attributes.value: 2020-03-05T11:23:16Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8877:Cis_reg_DNA_852
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: fruit fly
attributes.tag: sample name
attributes.value: E-MTAB-8877:Cis_reg_DNA_852
attributes.tag: scientific_name
attributes.value: Drosophila melanogaster
attributes.tag: sex
attributes.value: mixed sex
attributes.tag: strain
attributes.value: DGRP 852