ERX4489138 E-MTAB-9363:HT-184-d85-duo_p ERP123686 PRJEB40087 scRNA-seq of human fetal lung and intestine tissue ERS5040410 SAMEA7279808 HT-184-d85-duo_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT Use of human tissue was reviewed and approved by The University of Michigan Institutional Review Board (IRB). De-identified human fetal lung and intestine tissue was obtained from the University of Washington Laboratory of Developmental Biology. Tissue was shipped overnight in Belzer-UW Cold Storage Solution (ThermoFisher, NC0952695) with cold packs. Cell dissociations were carried out similar to previously published methods (Miller et al., 2020). To dissociate human fetal tissue to single cells, tissue was mechanically minced into small fragments, and in a petri dish filled with ice-cold 1X HBSS (with Mg2+, Ca2+). This tissue was then transferred to a 15 mL conical tube. Dissociation enzymes and reagents from the Neural Tissue Dissociation Kit (Miltenyi, cat. no. 130-092-628) were used, and all incubation steps were carried out in a refrigerated centrifuge pre-chilled to 10ºC unless otherwise stated. All tubes and pipette tips used to handle cell suspensions were pre-washed with 1% BSA in HBSS to prevent adhesion of cells to the plastic. Tissue was treated for 15 minutes at 10ºC with Mix 1. Mix 2 was added to the digestion, and tissue was incubated for 10 minute increments at 10ºC until digestion was complete. After each 10 minute incubation, tissue was agitated using a P1000, and tissue digestion was visually assessed under a stereo microscope. This process continued until the tissue was fully digested. Cells were filtered through a 70 µm filter coated with 1% BSA in 1X HBSS, spun down at 500g for 5 minutes at 10ºC and resuspended in 500µl 1X HBSS (with Mg2+, Ca2+). 1 mL Red Blood Cell Lysis buffer (Roche cat. No 11814389001) was then added to the tube and the cell mixture was placed on a rocker for 15 minutes at 4ºC. Cells were spun down (500g for 5 minutes at 10ºC), and washed twice by suspension in 2 mLs of HBSS + 1% BSA followed by centrifugation. Cells were counted using a hemocytometer, then spun down and resuspended (if necessary) to reach a concentration of 1000 cells/µL and kept on ice. Single cell droplets were immediately prepared on the 10x Chromium according to manufacturer instructions at the University of Michigan The Advanced Genomics Core, with a target of capturing 5,000 cells. Single cell libraries were prepared using the Chromium Next GEM Single Cell 3' Library Construction Kit v2 according to manufacturer instructions. Immediately after tissue dissociation, single cell libraries were prepared on the 10x Chromium with a target of 5,000 cells. Chromium Single Cell 3' Library & Gel Bead Kit v2, 16 rxns PN-120237 was used. Immediately after tissue dissociation, single cell libraries were prepared on the 10x Chromium with a target of 5,000 cells. Chromium Single Cell 3' Library & Gel Bead Kit v2, 16 rxns PN-120237 was used. Illumina HiSeq 4000 Experimental Factor: age 12.1 Experimental Factor: sampling site full thickness duodenum ERX4489139 E-MTAB-9363:HT-223_132day_DistalLung_p ERP123686 PRJEB40087 scRNA-seq of human fetal lung and intestine tissue ERS5040411 SAMEA7279809 HT-223_132day_DistalLung_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT Use of human tissue was reviewed and approved by The University of Michigan Institutional Review Board (IRB). De-identified human fetal lung and intestine tissue was obtained from the University of Washington Laboratory of Developmental Biology. Tissue was shipped overnight in Belzer-UW Cold Storage Solution (ThermoFisher, NC0952695) with cold packs. Cell dissociations were carried out similar to previously published methods (Miller et al., 2020). To dissociate human fetal tissue to single cells, tissue was mechanically minced into small fragments, and in a petri dish filled with ice-cold 1X HBSS (with Mg2+, Ca2+). This tissue was then transferred to a 15 mL conical tube. Dissociation enzymes and reagents from the Neural Tissue Dissociation Kit (Miltenyi, cat. no. 130-092-628) were used, and all incubation steps were carried out in a refrigerated centrifuge pre-chilled to 10ºC unless otherwise stated. All tubes and pipette tips used to handle cell suspensions were pre-washed with 1% BSA in HBSS to prevent adhesion of cells to the plastic. Tissue was treated for 15 minutes at 10ºC with Mix 1. Mix 2 was added to the digestion, and tissue was incubated for 10 minute increments at 10ºC until digestion was complete. After each 10 minute incubation, tissue was agitated using a P1000, and tissue digestion was visually assessed under a stereo microscope. This process continued until the tissue was fully digested. Cells were filtered through a 70 µm filter coated with 1% BSA in 1X HBSS, spun down at 500g for 5 minutes at 10ºC and resuspended in 500µl 1X HBSS (with Mg2+, Ca2+). 1 mL Red Blood Cell Lysis buffer (Roche cat. No 11814389001) was then added to the tube and the cell mixture was placed on a rocker for 15 minutes at 4ºC. Cells were spun down (500g for 5 minutes at 10ºC), and washed twice by suspension in 2 mLs of HBSS + 1% BSA followed by centrifugation. Cells were counted using a hemocytometer, then spun down and resuspended (if necessary) to reach a concentration of 1000 cells/µL and kept on ice. Single cell droplets were immediately prepared on the 10x Chromium according to manufacturer instructions at the University of Michigan The Advanced Genomics Core, with a target of capturing 5,000 cells. Single cell libraries were prepared using the Chromium Next GEM Single Cell 3' Library Construction Kit v2 according to manufacturer instructions. Immediately after tissue dissociation, single cell libraries were prepared on the 10x Chromium with a target of 5,000 cells. Chromium Single Cell 3' Library & Gel Bead Kit v2, 16 rxns PN-120237 was used. Immediately after tissue dissociation, single cell libraries were prepared on the 10x Chromium with a target of 5,000 cells. Chromium Single Cell 3' Library & Gel Bead Kit v2, 16 rxns PN-120237 was used. Illumina HiSeq 4000 Experimental Factor: age 18.9 Experimental Factor: sampling site distal lung ERX4489140 E-MTAB-9363:HT-236-day132-ileum_p ERP123686 PRJEB40087 scRNA-seq of human fetal lung and intestine tissue ERS5040412 SAMEA7279810 HT-236-day132-ileum_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT Use of human tissue was reviewed and approved by The University of Michigan Institutional Review Board (IRB). De-identified human fetal lung and intestine tissue was obtained from the University of Washington Laboratory of Developmental Biology. Tissue was shipped overnight in Belzer-UW Cold Storage Solution (ThermoFisher, NC0952695) with cold packs. Cell dissociations were carried out similar to previously published methods (Miller et al., 2020). To dissociate human fetal tissue to single cells, tissue was mechanically minced into small fragments, and in a petri dish filled with ice-cold 1X HBSS (with Mg2+, Ca2+). This tissue was then transferred to a 15 mL conical tube. Dissociation enzymes and reagents from the Neural Tissue Dissociation Kit (Miltenyi, cat. no. 130-092-628) were used, and all incubation steps were carried out in a refrigerated centrifuge pre-chilled to 10ºC unless otherwise stated. All tubes and pipette tips used to handle cell suspensions were pre-washed with 1% BSA in HBSS to prevent adhesion of cells to the plastic. Tissue was treated for 15 minutes at 10ºC with Mix 1. Mix 2 was added to the digestion, and tissue was incubated for 10 minute increments at 10ºC until digestion was complete. After each 10 minute incubation, tissue was agitated using a P1000, and tissue digestion was visually assessed under a stereo microscope. This process continued until the tissue was fully digested. Cells were filtered through a 70 µm filter coated with 1% BSA in 1X HBSS, spun down at 500g for 5 minutes at 10ºC and resuspended in 500µl 1X HBSS (with Mg2+, Ca2+). 1 mL Red Blood Cell Lysis buffer (Roche cat. No 11814389001) was then added to the tube and the cell mixture was placed on a rocker for 15 minutes at 4ºC. Cells were spun down (500g for 5 minutes at 10ºC), and washed twice by suspension in 2 mLs of HBSS + 1% BSA followed by centrifugation. Cells were counted using a hemocytometer, then spun down and resuspended (if necessary) to reach a concentration of 1000 cells/µL and kept on ice. Single cell droplets were immediately prepared on the 10x Chromium according to manufacturer instructions at the University of Michigan The Advanced Genomics Core, with a target of capturing 5,000 cells. Single cell libraries were prepared using the Chromium Next GEM Single Cell 3' Library Construction Kit v2 according to manufacturer instructions. Immediately after tissue dissociation, single cell libraries were prepared on the 10x Chromium with a target of 5,000 cells. Chromium Single Cell 3' Library & Gel Bead Kit v2, 16 rxns PN-120237 was used. Immediately after tissue dissociation, single cell libraries were prepared on the 10x Chromium with a target of 5,000 cells. Chromium Single Cell 3' Library & Gel Bead Kit v2, 16 rxns PN-120237 was used. Illumina NovaSeq 6000 Experimental Factor: age 18.9 Experimental Factor: sampling site full thickness ileum