characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-08-01T00:16:43Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-08-01T00:16:43Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA111329673
characteristics.characteristic: External Id
characteristics.text: Institut de Genomique Fonctionnelle de Lyon
characteristics.characteristic: INSDC center name
characteristics.text: 2023-08-01T00:16:43Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-08-01T00:16:43Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS13427237
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12146:yw_Rep2
characteristics.characteristic: Submitter Id
characteristics.text: 5 to 8
characteristics.unit: hour
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: fruit fly
characteristics.characteristic: common name
characteristics.text: Protocols: For collection of embryos, freshly hatched adult flies of the appropriate genotype were placed in embryo collection vials with standard apple cap plates. Embryos were collected on apple juice agar plates at 25 °C from 5 to 8 hours (after 3 pre-lays of 1 hour), dechorionated using 50% bleach, and washed alternately with water and PBS + 0.1% Triton X-100. The embryos were covalently crosslinked in 1.8% formaldehyde for 15 min, quenched for 5 min with 2M Tris-HCl pH7.5, then crosslinked again with 3 mM DSG for 45min, quenched as above and stored at -80°C. Nucleic acid was extracted as per the Micro-C protocol in Hsieh et al., 2020, with appropriate modifications for Drosophila embryos. Nuclear extraction was carried out as described in Ghavi-Helm et al., 2014 using cold MB#1 buffer (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 mM CaCl2, freshly added 0.2% NP-40 and 1x PIC) to resuspend the embryos and extract the nuclei by Dounce homogenization. Nuclei from each sample (~600ng) was then treated with an appropriate concentration of Micrococcal Nuclease (~45U) to yield a 90% mononucleosome / 10% dinucleosome ratio. Micro-C libraries were constructed based on Hsieh et al., 2020, with appropriate modifications for Drosophila embryos. For each sample, chromatin obtained from 7 MNase reactions were combined and taken forward for end-chewing, end-labelling, and proximity ligation. After reverse cross-linking, 150-200 ng of the obtained chromatin was size-selected for ligated mononucleosomes (250-400 bp) on a 3.5% NuSieve agarose gel. The size-selected chromatin was then pulled-down with 25 µl of streptavidin beads, and taken forward for library preparation using the NEBNext Ultra II DNA Library Prep Kit for Illumina.
characteristics.characteristic: description
characteristics.text: embryonic stage 10 to 11
characteristics.characteristic: developmental stage
characteristics.text: y[1] w[1118]
characteristics.characteristic: genotype
characteristics.text: mix pool of embryos
characteristics.characteristic: individual
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Drosophila melanogaster
characteristics.characteristic: organism
characteristics.text: Drosophila melanogaster
characteristics.characteristic: organism
characteristics.text: whole organism
characteristics.characteristic: organism part
characteristics.text: Drosophila melanogaster
characteristics.characteristic: scientific_name
characteristics.text: mixed sex
characteristics.characteristic: sex
characteristics.text: wild type
characteristics.characteristic: strain
characteristics.text: yw_Rep2
characteristics.characteristic: title