biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsthomas cokelaerNextSeq 2000RNA-seq of total RNAMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15420Hamster (ham) and mouse (m) bone marrow-derived macrophages (BMDMs) exhibit differential susceptibility to microbial infections, including Leishmania donovani. We hypothesize that intrinsic biological differences between these rodent macrophages contribute to this variability and ultimately to disease progression. To investigate this, we performed RNA sequencing on ham- and mBMDMs collected at 24 hours and 3 days post-differentiation. This allowed us to evaluate temporal changes in gene expression within each BMDM system and identify host determinants that may influence the establishment of intracellular infection.biostudies-arrayexpressNucleic Acid Extraction - The total RNA extraction was performed according to instructions provided with the Macherey Nagel NucleoSpin® RNA plus kit and RNA integrity was assessed using Nanodrop and the Agilent 2100 Bioanalyzer.Sequencing - nucleic acid sequencing protocol: RNA sequencing was performed on the Illumina NextSeq 2000 platform using single-end 75bpSample Collection - Ham- and mBMDMs were washed with warm PBS-A and scraped with 350 µl of LPB lysis buffer provided with the Macherey Nagel NucleoSpin® RNA plus kit at desired time points. The recovered lysates were passed through a 1 ml syringe/26G needle and stored at -80°C until RNA extraction.Library Construction - Libraries were prepared from 250 ng of RNA using Illumina Stranded mRNA Prep (Illumina) following the manufacturer’s protocol. Briefly, mRNA was captured by oligo-dT magnetic beads, fragmented and reverse transcribed. Sample-specific barcodes were ligated to the cDNA which was then amplified by 15 cycles of PCR. Note only the first cDNA strand was amplified. Purification of unbound adaptors and primers was done on AMP beads (Beckman Coulter) added to samples in a 0,8:1 ratio. The resulting stranded libraries comprised fragments from 200 to 1000 bp with a peak around 490 bp as visualized on a 5300 Fragment Analyzer (Agilent Technologies). Libraries were pooled, purified on AMP beads as above, diluted to 0,8 nM and sequenced on a NextSeq 2000 system (Illumina) using a P3 50-cycle sequencing kit. The yield was 1200 mln 67- bp single-end reads (30 – 60 mln reads per sample)OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesPascale Pescherthomas cokelaerPaul JenkinsfalseIntrinsic Differences in Hamster and Mouse Macrophages BiologyHamster (ham) and mouse (m) bone marrow-derived macrophages (BMDMs) exhibit differential susceptibility to microbial infections, including Leishmania donovani. We hypothesize that intrinsic biological differences between these rodent macrophages contribute to this variability and ultimately to disease progression. To investigate this, we performed RNA sequencing on ham- and mBMDMs collected at 24 hours and 3 days post-differentiation. This allowed us to evaluate temporal changes in gene expression within each BMDM system and identify host determinants that may influence the establishment of intracellular infection.2026-05-14T00:00:00Z2026-05-14T01:01:43.724Z2025-07-30T15:38:24.777ZE-MTAB-15420ERP177495EFO_0002944EFO_0004170EFO_0009653EFO_0005518EFO_0004184