characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-07-12T00:19:24Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-07-12T00:19:24Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA113399637
characteristics.characteristic: External Id
characteristics.text: Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
characteristics.characteristic: INSDC center name
characteristics.text: 2023-07-12T00:19:24Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-07-12T00:19:24Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS15394784
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12888:Nuc_4_Rep3
characteristics.characteristic: Submitter Id
characteristics.text: 0
characteristics.unit: day
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: neuron of crebral cortex
characteristics.characteristic: cell_type
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Primary cortical neurons were prepared from P0 mouse pups (C57B/6), and cultured as previously described (Kaech, 2006). 106 primary neurons were plated per a Millicell cell culture insert (6-well, Millipore MCRP06H48), coated with poly-D-Lysine and laminin. Separation into soma and neurites was performed using a cotton swab as described (Zappulo, 2017) and further separation of soma on nuclear and cytoplasmic fractions was performed using NE-PER Nuclear and Cytoplasmic Extraction Kit (Thermo 78833) following manufacturer’s instructions. Primary cortical were grown in the presence of 200nM 4-thiouridine (s4U) for 24 hours, then s4U was replaced with an excess (20mM) of unmodified uridine (U) and RNA was isolated at the indicated time points, where 0 hours is the time of s4U withdrawal. Isolated RNA was subjected to alkylation by heating to 50°C in the presence of 50 µg/µl Iodoacetamide for 15 min and cleaned up using Ampure beads. RNA was extracted from Trifast using 2-step chloroform extraction and isopropanol precipitation. After alkylation and an additional RNA cleanup step using Ampure beads RNA samples were quantified using qubit and analysed for integrity with tapestation. TrueSeq stranded mRNA Library kit; 1ul of 1:300 ERCC1 spike-in was added to 49ul initial solution with 100ng total RNA.; Final PCR was done with 13-17 cycles’ reaction
characteristics.characteristic: description
characteristics.text: neonate
characteristics.characteristic: developmental stage
characteristics.text: nucleus
characteristics.characteristic: fraction
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: brain
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: mixed
characteristics.characteristic: sex
characteristics.text: C57BL/6
characteristics.characteristic: strain
characteristics.text: Nuc_4_Rep3
characteristics.characteristic: title