biostudies-arrayexpressAleksandra KolodziejczykMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14263In this study we compared three different groups of mice to understand the role of antibiotics and microbial colonisation during early life. (1) young mice that were untreated and sacrificed pre-weaning, 12 days after birth, (2) control mice were also untreated and sacrificed 44 days after birth, these mice were were weaned at 24 days old and (3) recolonised mice that were treated with broad-spectrum antibiotics (ampicillin, vancomycin, neomycin and metronidazole) from 14 days to 35 days of age. At 37 days mice were gavaged with faecal microbial matter prepared from control mice before being sacrificed at 44 days of age. They were also weaned at 24 days old.biostudies-arrayexpressLibrary Construction - according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User GuideNucleic Acid Extraction - according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User GuideSequencing - according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User GuideSample Collection - Colon lamina propria. Whole colon was dissected from the animal and cut longitudinally to remove contents and tissue was vortexed in clean 4 °C Ca/Mg-free PBS to wash it. This was repeated until solution was clear. 10 ml of 37 °C Dissociation Buffer (Ca/Mg-free HBSS, 3 mM EDTA pH 8, 1 mM DTT) was added and incubated shaking at 37 °C for 15 min to dissociate epithelial layer. Then tissue was vortexed epithelial layer stripping and moved to fresh 10ml of Dissociation Buffer and incubated shaking at 37 °C for 20 min. Then, the tissue was placed in cold Ca/Mg-free HBSS, washed twice using vortex and dried on clean paper. To disintegrate colon tissue was first chopped with scissors and subsequently incubated shaking in Digestion Buffer (RPMI, 10% FCS, 0.8 mg/ml collagenase D, 1.6 mg/ml dispase) at 37 °C for 35 min. 10 ml of cold Ca/Mg-free HBSS was then added to stop digestion and cells were passed through 85-μm metal mesh. Then cells were collected by centrifugation at 500g for 8 min at 4 °C. To lyse erythrocytes pellets were resuspended in 1 ml ACK buffer and incubated for 1 min at room temperature. Then 10 ml of Ca/Mg-free PBS was added, cells were centrifuged at 500g for 8 min. To remove dead cells and to ensure depletion of epithelium we resuspended the pellet in 100 μl of Ca/Mg-free PBS with 1% FCS and incubated for 5 min with 1μg/ml anti-CD16/32 (Biolegend) to block Fc receptors before adding the 1:100 EPCAM APC-Cy7 antibody (G8.8, Biolegend). The cells were incubated for 30 min on ice, then 1:10.000 dilution of DAPI was added and stained for additional 3 min. Then 10 ml of Ca/Mg-free PBS was added, and the cells were centrifuged for 8 min at 500g. The supernatant was removed,and the cells were resuspended in PBS, filtered through a 40-μm mesh and DAPI negative and EPCAM negative cells were sorted on BD FACSAria III. Sorted cells were then centrifuged 8 min at 500g, resuspended in Ca/Mg-free PBS with 0.04% BSA and counted.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Data was analysed using Cell Ranger pipeline v6.0.0 and mapped to mouse genomeData Transformation - Data was analysed using Cell Ranger pipeline v6.0.0 and mapped to mouse genomeMetabolomicsUnknownTranscriptomicsGenomicsProteomics10x Genomics ChromiumIllumina NovaSeq 6000manualRNA-seq of coding RNA from single cellsMus musculusAleksandra KolodziejczykKolodziejczyk KolodziejczykfalseThe impact of microbial colonisation on intestinal macrophagesIn this study we compared three different groups of mice to understand the role of antibiotics and microbial colonisation during early life. (1) young mice that were untreated and sacrificed pre-weaning, 12 days after birth, (2) control mice were also untreated and sacrificed 44 days after birth, these mice were were weaned at 24 days old and (3) recolonised mice that were treated with broad-spectrum antibiotics (ampicillin, vancomycin, neomycin and metronidazole) from 14 days to 35 days of age. At 37 days mice were gavaged with faecal microbial matter prepared from control mice before being sacrificed at 44 days of age. They were also weaned at 24 days old.2026-07-18T00:00:00Z2026-07-18T01:01:02.462Z2024-07-22T10:10:12.269ZE-MTAB-14263ERP162180EFO_0002944EFO_0004170EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184