SRX10201257 GSM5123132 SRP308745 SRS8347737 GSM5123132 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123132 GSM5123132 GEO Accession GSM5123132 SRX10201258 GSM5123133 SRP308745 SRS8347738 GSM5123133 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123133 GSM5123133 GEO Accession GSM5123133 SRX10201259 GSM5123134 SRP308745 SRS8347741 GSM5123134 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123134 GSM5123134 GEO Accession GSM5123134 SRX10201260 GSM5123135 SRP308745 SRS8347740 GSM5123135 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123135 GSM5123135 GEO Accession GSM5123135 SRX10201261 GSM5123136 SRP308745 SRS8347739 GSM5123136 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123136 GSM5123136 GEO Accession GSM5123136 SRX10201262 GSM5123137 SRP308745 SRS8347742 GSM5123137 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123137 GSM5123137 GEO Accession GSM5123137 SRX10201263 GSM5123138 SRP308745 SRS8347743 GSM5123138 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123138 GSM5123138 GEO Accession GSM5123138 SRX10201264 GSM5123139 SRP308745 SRS8347744 GSM5123139 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123139 GSM5123139 GEO Accession GSM5123139 SRX10201265 GSM5123140 SRP308745 SRS8347746 GSM5123140 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123140 GSM5123140 GEO Accession GSM5123140 SRX10201266 GSM5123141 SRP308745 SRS8347745 GSM5123141 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123141 GSM5123141 GEO Accession GSM5123141 SRX10201267 GSM5123142 SRP308745 SRS8347747 GSM5123142 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123142 GSM5123142 GEO Accession GSM5123142 SRX10201268 GSM5123143 SRP308745 SRS8347748 GSM5123143 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123143 GSM5123143 GEO Accession GSM5123143 SRX10201269 GSM5123144 SRP308745 SRS8347750 GSM5123144 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123144 GSM5123144 GEO Accession GSM5123144 SRX10201270 GSM5123145 SRP308745 SRS8347749 GSM5123145 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123145 GSM5123145 GEO Accession GSM5123145 SRX10201271 GSM5123146 SRP308745 SRS8347751 GSM5123146 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123146 GSM5123146 GEO Accession GSM5123146 SRX10201272 GSM5123147 SRP308745 SRS8347752 GSM5123147 RNA-Seq TRANSCRIPTOMIC cDNA Total cellular RNAs were extracted from ileal organods using RNeasy Mini Kit (Qiagen). The RNA integrity was assessed on a 2100 Bioanalyzer (Agilent). A double-stranded cDNA library was created using 500 ng of total RNA (measured by picogreen), preparing the fragments for hybridization onto a flowcell. An ERCC RNA Spike-In Control Mix 1 was added to each sample according to the manufacturer's protocol. First, cytoplasmic and mitochondrial ribosomal RNA was removed from the total RNA samples using Illumina's Epidemiology-Specific RiboZero rRNA removal protocol. Then cDNA was generated using the fragmented and rRNA-depleted total RNA using random primers. During second-strand synthesis, deoxythymidine triphosphate (dTTP) was replaced with deoxyuridine triphosphate (dUTP) which quenches the second strand during amplification, thereby achieving strand specificity. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3′ end, and finally ligating unique adapters to the ends for PCR amplification. Paired end sequencing (2 × 100 bp) was performed on an Illumina HiSeq for a depth of 30 million paired end reads (a total of 60 million reads) per RNA sample. Illumina HiSeq 4000 gds 305123147 GSM5123147 GEO Accession GSM5123147