characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-05-14T00:14:59Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-05-14T00:14:59Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110460921
characteristics.characteristic: External Id
characteristics.text: EMBL
characteristics.characteristic: INSDC center name
characteristics.text: 2023-05-14T00:14:59Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-05-14T00:14:59Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12558949
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12070:Hi-C_WE_2-4h_2
characteristics.characteristic: Submitter Id
characteristics.text: 2 to 4
characteristics.unit: hour
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: fruit fly
characteristics.characteristic: common name
characteristics.text: Protocols: Wildtype Drosophila melanogaster flies were grown in population cages at 25 degr. Staged 2 hr populations of embryos were collected and aged at 25 degr till the required stage of development. Two independent collections were performed for each timepoint. The collected embryos were dechorionated using 50% bleach and formaldehyde fixed in 10 ml cross-linking solution (50 mM Hepes, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8 % formaldehyde, pH 8.0) and 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. 1g of frozen embryos were dounce-homogenized, 20 times with a loose pestle and 10 times with a tight pestle, in 10 ml of chilled HB buffer (15 mM Tris-HCl (pH 7.4), 0.34 M sucrose, 15 mM NaCl, 60 mM KCl, 0.2 mM EDTA and 0.2 mM EGTA) on ice. The lysate was filtered through 2 layers of Miracloth and spun at 3,500g for 10 min to pellet the nuclei. The nuclei were then washed in 10 ml of chilled HB buffer, spun at 3,500g for 10 min and resuspended in 3 ml of PBTB buffer (5% (wt/vol) BSA, 0.1% (vol/vol) Triton X-100 in PBS). The nuclei were dissociated by passing them ten times through a 20-G needle and then ten times through a 22-G needle using a 5-ml syringe, and filtered through a 20-�uem Sefar Nitex membrane. The total number of nuclei was estimated by microscopy, and 30 million nuclei aliquots were frozen in liquid nitrogen. Three aliquots of 30x106 nuclei in 2 biological replicates were used for each 3C template preparation. The Hi-C libraries were prepared as previously described (Sexton et al. 2012), using DpnII as restriction enzyme. The final library was prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions from at least 1 �g of DNA.
characteristics.characteristic: description
characteristics.text: stage 5-8
characteristics.characteristic: developmental stage
characteristics.text: egg laying
characteristics.characteristic: initial time point
characteristics.text: Drosophila melanogaster
characteristics.characteristic: organism
characteristics.text: Drosophila melanogaster
characteristics.characteristic: organism
characteristics.text: whole embryo
characteristics.characteristic: organism part
characteristics.text: Drosophila melanogaster
characteristics.characteristic: scientific_name
characteristics.text: mixed sex
characteristics.characteristic: sex
characteristics.text: OregonR
characteristics.characteristic: strain
characteristics.text: Hi-C_WE_2-4h_2
characteristics.characteristic: title