ERX5588771 E-MTAB-10492:LSD1KO_abx_m26_p ERP129173 PRJEB45052 scRNAseq of small intestine-derived lamina propria CD45+ cells from untreated wild type (WT), untreated intestinal epithelial specific LSD1 knockout (cKO), antibiotic-treated WT mice and antibiotic-treated cKO mice ERS6469190 SAMEA8784828 LSD1KO_abx_m26_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA Isolation of Lamina Propria lymphocytes was performed according to the protocol described in Webster et al, see reference below. Only modification was using PBS without calcium and magnesium instead of HBSS. After isolation according to the protocol, an extra step of cell sorting was done to remove any residual epithelial cell before performing scRNAseq on the CD45+ population. Briefly, isolated cells were incubated in PBS + 1%FBS + 2mM EDTA (flow buffer) along with DAPI, CD326 PE-Cy7 and CD45 PE-Cy5. Live CD45+ cells were selected on a DAPI- CD326- CD45+ basis and collected in RPMI 1640 + 10% FCS + 2mM Glutamine 2mM. Cells were then pelleted and resuspended in flow buffer at 1x10^6 cells/ml and brought to the genomics core on ice. Viability post-sorting was determined to be 85-90%. Untreated and antibiotics treated mice were isolated on different days, but sequenced at the same time. References: Webster HC, Andrusaite AT, Shergold AL, Milling SWF, Perona-Wright G. Isolation and functional characterisation of lamina propria leukocytes from helminth-infected, murine small intestine. J Immunol Methods. 2020 Feb;477:112702. doi: 10.1016/j.jim.2019.112702. Epub 2019 Nov 6. PMID: 31705860; PMCID: PMC6983935. Parental mice were treated ad libitum with a cocktail of antibiotics in drinking water freshly prepared every Monday, Wednesday and Friday. Ad libitum treatment of parental mice started 3-4 weeks before pup delivery and continued during the breastfeeding period. After weaning, pups were treated ad libitum with the same antibiotic cocktail up until tissue collection and cell isolation. Antibiotic cocktail: Ampicillin (1g/liter), Amoxicillin-Clavulanate (0,25g/liter), Neomycin (1g/liter), Gentamicin (1g/ liter), and Vancomycin (0.5g/liter) in drinking water. Added Sucralose (sweetener) 0,1g/liter to make the cocktail palatable. See nucleic acid library construction protocol Library preparation was done with 10X genomics Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 NextSeq 500 Experimental Factor: compound cocktail of 5 antibiotics Experimental Factor: dose ad libitum Experimental Factor: genotype Villin-Cre +; Lsd1f/f ERX5588772 E-MTAB-10492:WT_abx_m25_p ERP129173 PRJEB45052 scRNAseq of small intestine-derived lamina propria CD45+ cells from untreated wild type (WT), untreated intestinal epithelial specific LSD1 knockout (cKO), antibiotic-treated WT mice and antibiotic-treated cKO mice ERS6469191 SAMEA8784829 WT_abx_m25_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA Isolation of Lamina Propria lymphocytes was performed according to the protocol described in Webster et al, see reference below. Only modification was using PBS without calcium and magnesium instead of HBSS. After isolation according to the protocol, an extra step of cell sorting was done to remove any residual epithelial cell before performing scRNAseq on the CD45+ population. Briefly, isolated cells were incubated in PBS + 1%FBS + 2mM EDTA (flow buffer) along with DAPI, CD326 PE-Cy7 and CD45 PE-Cy5. Live CD45+ cells were selected on a DAPI- CD326- CD45+ basis and collected in RPMI 1640 + 10% FCS + 2mM Glutamine 2mM. Cells were then pelleted and resuspended in flow buffer at 1x10^6 cells/ml and brought to the genomics core on ice. Viability post-sorting was determined to be 85-90%. Untreated and antibiotics treated mice were isolated on different days, but sequenced at the same time. References: Webster HC, Andrusaite AT, Shergold AL, Milling SWF, Perona-Wright G. Isolation and functional characterisation of lamina propria leukocytes from helminth-infected, murine small intestine. J Immunol Methods. 2020 Feb;477:112702. doi: 10.1016/j.jim.2019.112702. Epub 2019 Nov 6. PMID: 31705860; PMCID: PMC6983935. Parental mice were treated ad libitum with a cocktail of antibiotics in drinking water freshly prepared every Monday, Wednesday and Friday. Ad libitum treatment of parental mice started 3-4 weeks before pup delivery and continued during the breastfeeding period. After weaning, pups were treated ad libitum with the same antibiotic cocktail up until tissue collection and cell isolation. Antibiotic cocktail: Ampicillin (1g/liter), Amoxicillin-Clavulanate (0,25g/liter), Neomycin (1g/liter), Gentamicin (1g/ liter), and Vancomycin (0.5g/liter) in drinking water. Added Sucralose (sweetener) 0,1g/liter to make the cocktail palatable. See nucleic acid library construction protocol Library preparation was done with 10X genomics Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 NextSeq 500 Experimental Factor: compound cocktail of 5 antibiotics Experimental Factor: dose ad libitum Experimental Factor: genotype Villin-Cre -; Lsd1f/+ ERX5588773 E-MTAB-10492:LSD1KO_H2O_m27_p ERP129173 PRJEB45052 scRNAseq of small intestine-derived lamina propria CD45+ cells from untreated wild type (WT), untreated intestinal epithelial specific LSD1 knockout (cKO), antibiotic-treated WT mice and antibiotic-treated cKO mice ERS6469192 SAMEA8784830 LSD1KO_H2O_m27_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA Isolation of Lamina Propria lymphocytes was performed according to the protocol described in Webster et al, see reference below. Only modification was using PBS without calcium and magnesium instead of HBSS. After isolation according to the protocol, an extra step of cell sorting was done to remove any residual epithelial cell before performing scRNAseq on the CD45+ population. Briefly, isolated cells were incubated in PBS + 1%FBS + 2mM EDTA (flow buffer) along with DAPI, CD326 PE-Cy7 and CD45 PE-Cy5. Live CD45+ cells were selected on a DAPI- CD326- CD45+ basis and collected in RPMI 1640 + 10% FCS + 2mM Glutamine 2mM. Cells were then pelleted and resuspended in flow buffer at 1x10^6 cells/ml and brought to the genomics core on ice. Viability post-sorting was determined to be 85-90%. Untreated and antibiotics treated mice were isolated on different days, but sequenced at the same time. References: Webster HC, Andrusaite AT, Shergold AL, Milling SWF, Perona-Wright G. Isolation and functional characterisation of lamina propria leukocytes from helminth-infected, murine small intestine. J Immunol Methods. 2020 Feb;477:112702. doi: 10.1016/j.jim.2019.112702. Epub 2019 Nov 6. PMID: 31705860; PMCID: PMC6983935. Parental mice were treated ad libitum with a cocktail of antibiotics in drinking water freshly prepared every Monday, Wednesday and Friday. Ad libitum treatment of parental mice started 3-4 weeks before pup delivery and continued during the breastfeeding period. After weaning, pups were treated ad libitum with the same antibiotic cocktail up until tissue collection and cell isolation. Antibiotic cocktail: Ampicillin (1g/liter), Amoxicillin-Clavulanate (0,25g/liter), Neomycin (1g/liter), Gentamicin (1g/ liter), and Vancomycin (0.5g/liter) in drinking water. Added Sucralose (sweetener) 0,1g/liter to make the cocktail palatable. See nucleic acid library construction protocol Library preparation was done with 10X genomics Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 NextSeq 500 Experimental Factor: compound drinking water Experimental Factor: dose ad libitum Experimental Factor: genotype Villin-Cre +; Lsd1f/f ERX5588774 E-MTAB-10492:WT_H2O_m28_p ERP129173 PRJEB45052 scRNAseq of small intestine-derived lamina propria CD45+ cells from untreated wild type (WT), untreated intestinal epithelial specific LSD1 knockout (cKO), antibiotic-treated WT mice and antibiotic-treated cKO mice ERS6469193 SAMEA8784831 WT_H2O_m28_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA Isolation of Lamina Propria lymphocytes was performed according to the protocol described in Webster et al, see reference below. Only modification was using PBS without calcium and magnesium instead of HBSS. After isolation according to the protocol, an extra step of cell sorting was done to remove any residual epithelial cell before performing scRNAseq on the CD45+ population. Briefly, isolated cells were incubated in PBS + 1%FBS + 2mM EDTA (flow buffer) along with DAPI, CD326 PE-Cy7 and CD45 PE-Cy5. Live CD45+ cells were selected on a DAPI- CD326- CD45+ basis and collected in RPMI 1640 + 10% FCS + 2mM Glutamine 2mM. Cells were then pelleted and resuspended in flow buffer at 1x10^6 cells/ml and brought to the genomics core on ice. Viability post-sorting was determined to be 85-90%. Untreated and antibiotics treated mice were isolated on different days, but sequenced at the same time. References: Webster HC, Andrusaite AT, Shergold AL, Milling SWF, Perona-Wright G. Isolation and functional characterisation of lamina propria leukocytes from helminth-infected, murine small intestine. J Immunol Methods. 2020 Feb;477:112702. doi: 10.1016/j.jim.2019.112702. Epub 2019 Nov 6. PMID: 31705860; PMCID: PMC6983935. Parental mice were treated ad libitum with a cocktail of antibiotics in drinking water freshly prepared every Monday, Wednesday and Friday. Ad libitum treatment of parental mice started 3-4 weeks before pup delivery and continued during the breastfeeding period. After weaning, pups were treated ad libitum with the same antibiotic cocktail up until tissue collection and cell isolation. Antibiotic cocktail: Ampicillin (1g/liter), Amoxicillin-Clavulanate (0,25g/liter), Neomycin (1g/liter), Gentamicin (1g/ liter), and Vancomycin (0.5g/liter) in drinking water. Added Sucralose (sweetener) 0,1g/liter to make the cocktail palatable. See nucleic acid library construction protocol Library preparation was done with 10X genomics Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 NextSeq 500 Experimental Factor: compound drinking water Experimental Factor: dose ad libitum Experimental Factor: genotype Villin-Cre -; Lsd1f/+