Intestinal epithelial inositol polyphosphate multikinase protects mice from experimental colitis via governing colonic tuft cell homeostasis

scRNA-seq libraries were prepared using the Smart-seq2 protocol

Section Single-Cell cDNA Synthesis and Sequencing Library Generation, offset —

scRNA-seq libraries were prepared using the Smart-seq2 protocol

Section Single-Cell cDNA Synthesis and Sequencing Library Generation, offset —

"instrument_model": {"NextSeq 550": 1203}

Section sample_values_with_sample_counts.instrument_model, offset —

aligned to the mouse reference genome (version mm10 from the University of California Santa Cruz)

Section Read alignment and gene quantification, offset —

transcriptomic single cell

Section library_source, offset —

GEO age characteristics: 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 weeks old; 11 wee

Section GEO family SOFT, offset —

For each experimental batch, 2 IPMKf/f mice and 2 IPMKΔIEC mice were used.

Section Single-Cell Transcriptomic Analysis Reveals the Heterogeneity of Colon Tuft Cells, offset —

Public on Oct 26 2022

Section series_status, offset —

GSE200284_Tuft_TPM.csv.gz

Section file_listing, offset —

A t-distributed stochastic neighbor embedding (t-SNE) plot showing that 2 independent experimental batches were overlaid well, indicating no batch effect.

Section Single-Cell Transcriptomic Analysis Reveals the Heterogeneity of Colon Tuft Cells, offset —

By unsupervised hierarchical clustering using Euclidean distance and Ward’s method, the tuft cell cluster was identified with higher expression of Dclk1, Siglecf, Il17rb, and Ptgs1

Section Identification of highly variable genes, cell clustering, and t-distributed stochastic neighbor embedding (t-SNE) visualization, offset —

Expression values of each gene were quantified as transcripts per million (TPM) using RSEM (version 1.3.3). TPMs were transformed to log 2 (TPM + 1).

Section Read alignment and gene quantification, offset —

cells with <500 detected genes and genes expressed in <5 cells were removed

Section Read alignment and gene quantification, offset —

colon

Section source_name, offset —

After filtering out cells with bad quality (eg, number of detected genes, <500), we analyzed 950 cells

Section Single-Cell Transcriptomic Analysis Reveals the Heterogeneity of Colon Tuft Cells, offset —

"sample_count": 1203

Section sample_count, offset —