SRX10412183 GSM5196863 SRP311673 SRS8533196 GSM5196863 RNA-Seq TRANSCRIPTOMIC cDNA Immune cells were isolated from lamina propria: tissue (cleared of crypts) was chopped finely with a scalpel and then incubated in 3ml of 1mg/ml collagenase-D (Merck, Cat. 11088866001) and 1mg/ml DNaseI in RPMI medium (ThermoFisherScientific, Cat. 21875091) in 6 well plates in an incubator shaker (80rpm) (VWR, Cat. 444-0732) for 20min at 37°C. Tissue pipetted up and down several times with a cut p1000 tip. The supernatant was passed through a 100μm strainer into 5% FBS in RPMI. Leftover tissue incubated again twice in 3ml collagenase-D/DNaseI RPMI solution in an incubator shaker (80rpm) for 30min at 37°C, collecting filtered supernatant. After the third incubation, the remaining tissue was smashed with a syringe plunger on a Falcon 40μm cell strainer (Corning, Cat. 352340) and washed with 5% FBS/RPMI to collect the maximum number of cells. The supernatant was centrifuged at 300g, 4°C for 5min. The pellet was re-suspended in 40% percoll (Sigma-Aldrich, Cat. P1644-1L) in RPMI. The cell suspension was carefully pipetted over 80% percoll in a falcon tube in order to create a gradient. The falcon tubes were centrifuged at 1600g, RT for 20min (centrifuge break disabled). The immune cells formed a white ring on the border of the two percoll concentrations: they were collected carefully and washed with FSM (2% FBS in PBS). The suspension was centrifuged at 450g, 4°C for 5min. Resulting pellet was resuspended in FSM and transferred for staining. The 10X Single Cell 3' v2 or v3.1 reagent kit (10X Genomics) was used for cell partitioning, cDNA amplification and library construction. NextSeq 500 gds 305196863 GSM5196863 GEO Accession GSM5196863 SRX10412184 GSM5196864 SRP311673 SRS8533197 GSM5196864 RNA-Seq TRANSCRIPTOMIC cDNA Immune cells were isolated from lamina propria: tissue (cleared of crypts) was chopped finely with a scalpel and then incubated in 3ml of 1mg/ml collagenase-D (Merck, Cat. 11088866001) and 1mg/ml DNaseI in RPMI medium (ThermoFisherScientific, Cat. 21875091) in 6 well plates in an incubator shaker (80rpm) (VWR, Cat. 444-0732) for 20min at 37°C. Tissue pipetted up and down several times with a cut p1000 tip. The supernatant was passed through a 100μm strainer into 5% FBS in RPMI. Leftover tissue incubated again twice in 3ml collagenase-D/DNaseI RPMI solution in an incubator shaker (80rpm) for 30min at 37°C, collecting filtered supernatant. After the third incubation, the remaining tissue was smashed with a syringe plunger on a Falcon 40μm cell strainer (Corning, Cat. 352340) and washed with 5% FBS/RPMI to collect the maximum number of cells. The supernatant was centrifuged at 300g, 4°C for 5min. The pellet was re-suspended in 40% percoll (Sigma-Aldrich, Cat. P1644-1L) in RPMI. The cell suspension was carefully pipetted over 80% percoll in a falcon tube in order to create a gradient. The falcon tubes were centrifuged at 1600g, RT for 20min (centrifuge break disabled). The immune cells formed a white ring on the border of the two percoll concentrations: they were collected carefully and washed with FSM (2% FBS in PBS). The suspension was centrifuged at 450g, 4°C for 5min. Resulting pellet was resuspended in FSM and transferred for staining. The 10X Single Cell 3' v2 or v3.1 reagent kit (10X Genomics) was used for cell partitioning, cDNA amplification and library construction. NextSeq 500 gds 305196864 GSM5196864 GEO Accession GSM5196864 SRX10412185 GSM5196865 SRP311673 SRS8533198 GSM5196865 RNA-Seq TRANSCRIPTOMIC cDNA Immune cells were isolated from lamina propria: tissue (cleared of crypts) was chopped finely with a scalpel and then incubated in 3ml of 1mg/ml collagenase-D (Merck, Cat. 11088866001) and 1mg/ml DNaseI in RPMI medium (ThermoFisherScientific, Cat. 21875091) in 6 well plates in an incubator shaker (80rpm) (VWR, Cat. 444-0732) for 20min at 37°C. Tissue pipetted up and down several times with a cut p1000 tip. The supernatant was passed through a 100μm strainer into 5% FBS in RPMI. Leftover tissue incubated again twice in 3ml collagenase-D/DNaseI RPMI solution in an incubator shaker (80rpm) for 30min at 37°C, collecting filtered supernatant. After the third incubation, the remaining tissue was smashed with a syringe plunger on a Falcon 40μm cell strainer (Corning, Cat. 352340) and washed with 5% FBS/RPMI to collect the maximum number of cells. The supernatant was centrifuged at 300g, 4°C for 5min. The pellet was re-suspended in 40% percoll (Sigma-Aldrich, Cat. P1644-1L) in RPMI. The cell suspension was carefully pipetted over 80% percoll in a falcon tube in order to create a gradient. The falcon tubes were centrifuged at 1600g, RT for 20min (centrifuge break disabled). The immune cells formed a white ring on the border of the two percoll concentrations: they were collected carefully and washed with FSM (2% FBS in PBS). The suspension was centrifuged at 450g, 4°C for 5min. Resulting pellet was resuspended in FSM and transferred for staining. The 10X Single Cell 3' v2 or v3.1 reagent kit (10X Genomics) was used for cell partitioning, cDNA amplification and library construction. NextSeq 500 gds 305196865 GSM5196865 GEO Accession GSM5196865 SRX10412186 GSM5196866 SRP311673 SRS8533199 GSM5196866 RNA-Seq TRANSCRIPTOMIC cDNA Immune cells were isolated from lamina propria: tissue (cleared of crypts) was chopped finely with a scalpel and then incubated in 3ml of 1mg/ml collagenase-D (Merck, Cat. 11088866001) and 1mg/ml DNaseI in RPMI medium (ThermoFisherScientific, Cat. 21875091) in 6 well plates in an incubator shaker (80rpm) (VWR, Cat. 444-0732) for 20min at 37°C. Tissue pipetted up and down several times with a cut p1000 tip. The supernatant was passed through a 100μm strainer into 5% FBS in RPMI. Leftover tissue incubated again twice in 3ml collagenase-D/DNaseI RPMI solution in an incubator shaker (80rpm) for 30min at 37°C, collecting filtered supernatant. After the third incubation, the remaining tissue was smashed with a syringe plunger on a Falcon 40μm cell strainer (Corning, Cat. 352340) and washed with 5% FBS/RPMI to collect the maximum number of cells. The supernatant was centrifuged at 300g, 4°C for 5min. The pellet was re-suspended in 40% percoll (Sigma-Aldrich, Cat. P1644-1L) in RPMI. The cell suspension was carefully pipetted over 80% percoll in a falcon tube in order to create a gradient. The falcon tubes were centrifuged at 1600g, RT for 20min (centrifuge break disabled). The immune cells formed a white ring on the border of the two percoll concentrations: they were collected carefully and washed with FSM (2% FBS in PBS). The suspension was centrifuged at 450g, 4°C for 5min. Resulting pellet was resuspended in FSM and transferred for staining. The 10X Single Cell 3' v2 or v3.1 reagent kit (10X Genomics) was used for cell partitioning, cDNA amplification and library construction. NextSeq 500 gds 305196866 GSM5196866 GEO Accession GSM5196866 SRX10412187 GSM5196867 SRP311673 SRS8533200 GSM5196867 RNA-Seq TRANSCRIPTOMIC cDNA Immune cells were isolated from lamina propria: tissue (cleared of crypts) was chopped finely with a scalpel and then incubated in 3ml of 1mg/ml collagenase-D (Merck, Cat. 11088866001) and 1mg/ml DNaseI in RPMI medium (ThermoFisherScientific, Cat. 21875091) in 6 well plates in an incubator shaker (80rpm) (VWR, Cat. 444-0732) for 20min at 37°C. Tissue pipetted up and down several times with a cut p1000 tip. The supernatant was passed through a 100μm strainer into 5% FBS in RPMI. Leftover tissue incubated again twice in 3ml collagenase-D/DNaseI RPMI solution in an incubator shaker (80rpm) for 30min at 37°C, collecting filtered supernatant. After the third incubation, the remaining tissue was smashed with a syringe plunger on a Falcon 40μm cell strainer (Corning, Cat. 352340) and washed with 5% FBS/RPMI to collect the maximum number of cells. The supernatant was centrifuged at 300g, 4°C for 5min. The pellet was re-suspended in 40% percoll (Sigma-Aldrich, Cat. P1644-1L) in RPMI. The cell suspension was carefully pipetted over 80% percoll in a falcon tube in order to create a gradient. The falcon tubes were centrifuged at 1600g, RT for 20min (centrifuge break disabled). The immune cells formed a white ring on the border of the two percoll concentrations: they were collected carefully and washed with FSM (2% FBS in PBS). The suspension was centrifuged at 450g, 4°C for 5min. Resulting pellet was resuspended in FSM and transferred for staining. The 10X Single Cell 3' v2 or v3.1 reagent kit (10X Genomics) was used for cell partitioning, cDNA amplification and library construction. NextSeq 500 gds 305196867 GSM5196867 GEO Accession GSM5196867 SRX10412188 GSM5196868 SRP311673 SRS8533201 GSM5196868 RNA-Seq TRANSCRIPTOMIC cDNA Immune cells were isolated from lamina propria: tissue (cleared of crypts) was chopped finely with a scalpel and then incubated in 3ml of 1mg/ml collagenase-D (Merck, Cat. 11088866001) and 1mg/ml DNaseI in RPMI medium (ThermoFisherScientific, Cat. 21875091) in 6 well plates in an incubator shaker (80rpm) (VWR, Cat. 444-0732) for 20min at 37°C. Tissue pipetted up and down several times with a cut p1000 tip. The supernatant was passed through a 100μm strainer into 5% FBS in RPMI. Leftover tissue incubated again twice in 3ml collagenase-D/DNaseI RPMI solution in an incubator shaker (80rpm) for 30min at 37°C, collecting filtered supernatant. After the third incubation, the remaining tissue was smashed with a syringe plunger on a Falcon 40μm cell strainer (Corning, Cat. 352340) and washed with 5% FBS/RPMI to collect the maximum number of cells. The supernatant was centrifuged at 300g, 4°C for 5min. The pellet was re-suspended in 40% percoll (Sigma-Aldrich, Cat. P1644-1L) in RPMI. The cell suspension was carefully pipetted over 80% percoll in a falcon tube in order to create a gradient. The falcon tubes were centrifuged at 1600g, RT for 20min (centrifuge break disabled). The immune cells formed a white ring on the border of the two percoll concentrations: they were collected carefully and washed with FSM (2% FBS in PBS). The suspension was centrifuged at 450g, 4°C for 5min. Resulting pellet was resuspended in FSM and transferred for staining. The 10X Single Cell 3' v2 or v3.1 reagent kit (10X Genomics) was used for cell partitioning, cDNA amplification and library construction. NextSeq 500 gds 305196868 GSM5196868 GEO Accession GSM5196868