biostudies-arrayexpressDaria BuninaMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16276The experiment was designed to study which genes are differentially expressed on mRNA level in MNK1 or MNK2 KO mice, focusing on synaptic compartment, and further correlate these genes with mis-expressed proteins in the same genotype mice. This would reveal whether MNK1 or MNK2 KOs mostly affect transcriptional or post-transcriptional programs in the neurons.biostudies-arrayexpressSample Collection - Samples for mRNA-seq experiment were collected from four-week-old male mice for each knockout and wild-type genotypes, used as biological replicates in the subsequent analyses. Cortex was rapidly dissected and homogenized in oxygenated Krebs buffer (118.5mM NaCl, 2.5mM CaCl2, 1.18mM KH2PO4, 1.18mM MgSO4, 3.8mM MgCl2, 24.9mM NaHCO3, 212.7mM Glucose in diethyl pyrocarbonate (DEPC) treated H2O) with protease and phosphatase inhibitors in a dunce grinder. The homogenate was passed through 2x 100µm pre-wet nylon filter (Merck Millipore, NY1H02500) using an 18G needle, followed by a second filtration with a 5µm pre-wet filter (Merck Millipore, NY0502500). The lysate was centrifuged for 10min 1000g 4°C. The synaptoneurosome pellet was washed 1x in 500µl Krebs buffer. The resulting pellet was snap-frozen in liquid nitrogen and stored at -70°C until further use.Nucleic Acid Extraction - Frozen synaptoneurosomes were resuspended in 600 mL TRIzol using a 22G syringe and were centrifuged for 10min 13 000g 4°C. Total RNA was isolated using the Direct-zol RNA microprep kit (Zymo Research, #R2062) and treated with DNAse, following the manufacturer's instructions.Sequencing - Libraries were sequenced on the Illumina NovaSeq X Plus platform using PE100 sequencing mode, with a target of 50 million reads per library.Library Construction - Double-indexed stranded mRNA-Seq libraries were prepared using the ILMN Stranded mRNA Library Prep Kit (Illumina, #20040534), starting from 250 ng of input material according to the manufacturer’s instructions.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Gene counts were produced with a featureCounts function from the subread v.2.0.3 (featureCounts -T 8 -s 2 -p --countReadPairs) and Ensembl GRCm39.109 annotation of all mouse genes. Provided count files are raw, non-normalized read counts.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNAMus musculusHanna HörnbergDaria BuninafalseRNA-seq of cortical synaptoneurosomes from MNK1 and MNK2 KO mice.The experiment was designed to study which genes are differentially expressed on mRNA level in MNK1 or MNK2 KO mice, focusing on synaptic compartment, and further correlate these genes with mis-expressed proteins in the same genotype mice. This would reveal whether MNK1 or MNK2 KOs mostly affect transcriptional or post-transcriptional programs in the neurons.2026-02-10T00:00:00Z2026-05-27T15:12:28.409Z2025-11-24T08:27:05.485ZE-MTAB-16276ERP185541EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184