title: GSM4829562: KO 2; Mus musculus; RNA-Seq
library_construction_protocol: For scRNA-seq: Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3' Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer's protocol. Briefly, an input of 10,000 cells was added to each channel of a chip with a recovery rate of 3000 cells. The cells were then partitioned into Gel Beads in Emulsion in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, tagmentation and 5' adaptor attachment. For total RNA-seq: Terminal ileum tissues were extracted and stored at -20°C in RNAlater. RNA from the terminal ileum of 6 weeks old Il22Ra1fl/fl;Defa6-cre+ and their littermate cre- mice was isolated using TRIZOL extraction methods as per manufacture instructions (Life Technologies). For scRNA-seq: Libraries were sequenced on an Illumina NextSeq 500. Alignment to the mm10 mouse genome and unique molecular identifier (UMI) collapsing was performing using the Cellranger toolkit (version 1.3.1, 10X Genomics). For each cell, we quantified the number of genes for which at least one UMI was mapped and then excluded all cells with fewer than 1,000 detected genes. For total RNA-seq: Illumina compatible Total RNA cDNA libraries with RiboZero Gold depletion were generated following the TruSeq Stranded Total RNA Reference Guide (Illumina Document #1000000040499v00, TruSeq Stranded Total RNA Gold Illumina Kit #20020598).