characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-07-07T00:23:12Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-07-07T00:23:12Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110356156
characteristics.characteristic: External Id
characteristics.text: EMBL
characteristics.characteristic: INSDC center name
characteristics.text: 2023-07-07T00:23:12Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-07-07T00:23:12Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12453868
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-11978:yw_NC14_rep1 (CTCF KO batch)
characteristics.characteristic: Submitter Id
characteristics.text: 2 to 3
characteristics.unit: hour
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: fruit fly
characteristics.characteristic: common name
characteristics.text: Protocols: Adult flies from specific genotypes were placed in medium-sized cages. After three 1 h pre-lays, a 1 h embryo laying was allowed on apple juice agar plates with yeast paste. 2 hours later, embryos were immediately dechorionated using 50% bleach transferred to a 1.5ml tube containing ice-cold PBTr (PBS + 0.1 % TritonX-100). Embryos at NC14 were then manually selected under a stereoscope based on morphological features. 100 embryos per replicate were selected and transferred to a new 1.5ml tube. The PBTr was removed by pipetting, and the embryos were snap-frozen in liquid nitrogen. Fly embryos were homogenised in TRI Reagent (Sigma-Aldrich) using pestles and a cordless motor for pellet mixing and total RNA extraction was performed according to the manufacturer's instructions. Remaining DNA was digested using RNase-free DNase I (Roche), followed by a clean up using the Agencourt RNAClean XP kit (Beckman Coulter) according to the manufacturer's protocol. Poly(A) mRNA isolation and fragmentation were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer's instruction manual E7420, Chapter 1. 1 �g total RNA was used as starting material and the protocol optimised for 200 bp RNA inserts was followed. RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina according to the manufacturer's instruction manual E7420, Chapter 1. For library enrichment, 12 PCR cycles were used. Indexed RNA-seq libraries were pooled in an equimolar ratio and paired-end sequenced with a read length of 75 bp on an Illumina NextSeq 500 High Output Flow Cell.
characteristics.characteristic: description
characteristics.text: NC14
characteristics.characteristic: developmental stage
characteristics.text: none
characteristics.characteristic: genetic modification
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: egg laying
characteristics.characteristic: initial time point
characteristics.text: not applicable
characteristics.characteristic: isolate
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: yw_NC14_rep1 (CTCF KO batch)
characteristics.characteristic: title