Table 2 Summary of the scRNA-seq studies in the intestine
From: Intestinal cellular heterogeneity and disease development revealed by single-cell technology
Organism | Sample type | Sample source | Cell type | Library preparation method | Cell number | Data resource | Reference |
|---|---|---|---|---|---|---|---|
Mus musculus | Jejunum | Labeled stem cells | Short-term and long-term label-retaining stem cells | Fluidigm | 558 | Supplementary Table 2 | (Li et al., 2016) |
Mus musculus | Jejunum | Wildtype mice | Epithelial, mesenchymal and immune cells | MARS-seq | 329 | GSE134479 | (Bahar Halpern et al., 2020) |
Mus musculus | Jejunum | Stem cells | Prox1-GFP+, Bmi1-GFP+, Lgr5-eGFP+, and Lgr5-eGFP− cells | 10X Chromium | 3,521 | GSE99457 | (Yan et al., 2017) |
Mus musculus | Ileum | Massive small bowel resection | Epithelial cells | 10X Chromium | 19,245 | GSE130113 | (Seiler et al., 2019) |
Mus musculus | Small intestine | Wildtype mice | Crypt cells | C1 | 76 | GSE146783 | (Sato et al., 2020) |
Mus musculus | Small intestine | Labeled epithelial cells | Bmi1, Hopx or Lgr5 labeled cells | Fluidigm | 1,033 | Supplementary Table 2 | (Li et al., 2014) |
Mus musculus | Small intestine | Labeled epithelial cells | Intestinal preproglucagon-expressing cells | Smart-seq2 | 288 | Not described | (Glass et al., 2017) |
Mus musculus | Small intestine | Wildtype mice | Epithelial cells | 10X Chromium | 7,216 | GSE92332 | (Haber et al., 2017) |
Mus musculus | Small intestine | Stem cells | Lgr5high cells | Smart-seq | 245 | GSE90856 | (Barriga et al., 2017) |
Mus musculus | Small intestine | Stem cell depleted and normal epithelium | Epithelial cells | 10X Chromium | 192 | Not described | (Tetteh et al., 2016) |
Mus musculus | Small intestine | Lgr5-eGFP+ intestinal stem cells | Stem cells | 10X Chromium | 13,247 | GSE92865 | (Yan et al., 2017) |
Mus musculus | Small intestine | Wildtype and irradiated mice | Epithelial cells | 10X Chromium | 6,644 | GSE123516 | (Ayyaz et al., 2019) |
Mus musculus | Small intestine | Small intestine mucositis | Epithelial cells | 10X Chromium | 12,653 | GSE131630 | (Zhao et al., 2020) |
Mus musculus | Small intestine | Wildtype and Lats1/2 knockout mice | Pdgfrβ+ intestinal stromal cells and lymphatic endothelial cells | 10X Chromium | 7,906 | GSE124488 | (Hong et al., 2020) |
Mus musculus | Small intestine | Normal diet and high-fat/high-sugar diet mice | Epithelial cells | 10X Chromium | 27,687 | GSE147319 | (Aliluev et al., 2021) |
Mus musculus | Small intestine | Wildtype mice and β7-KO mice | Epithelial cells | 10X Chromium | 13,352 for WT; 10,763 for β7-KO | OEP000370 | (Chen et al., 2021a) |
Mus musculus | Small intestine | Wildtype; FltpZV/+; Foxa2FVF/FVF mice | Epithelial cells | 10X Chromium | 60,000 | GSE152325 | (Bottcher et al., 2021) |
Mus musculus | Small intestine | Wildtype crypts in Red2-KrasG12D and Red2-PIK3CAH1047R mice | Epithelial, mesenchymal and immune cells | 10X Chromium | 21,183 | E-MTAB-8656 | (Yum et al., 2021) |
Mus musculus | Small intestine | Wildtype mice | Epithelial cells | MARS-seq | Not described | GSE178586 | (Zinina et al., 2022) |
Mus musculus | Small intestine and colon | Casp3/7ΔIEC mice and Casp3/7FL/FL littermates | Epithelial cells and immune cells | 10X Chromium | 7,584 Casp3/7 fl/fl cells and 11,956 Casp3/7ΔIEC cells | GSE183885 | (Ghazavi et al., 2022) |
Mus musculus | Distal small intestine and colon | Muc2-mCherry mice | Goblet cells | 10X Chromium | 6123 cells for the colon and 3552 cells for the small intestine | GSE144436 | (Nystrom et al., 2021) |
Mus musculus | Colon | Wildtype mice | Gli1+ stromal cells | 10X Chromium | 4,464 | GSE113043 | (Degirmenci et al., 2018) |
Mus musculus | Colon | LGR5+ lineage tracing and lethal injury (irradiation) mice | Regenerating crypt cells and Ascl2-deficient colonic stem cells | 10X Chromium | 3,254 | GSE130822 | (Murata et al., 2020) |
Mus musculus | Colon | Wildtype mice | Pdgfra+ endothelial cells and epithelial cells | 10X Chromium | 6,358 | GSE130681 | (McCarthy et al., 2020c) |
Mus musculus | Colon | NeuroD1-Cre x Rosa26-EYFP labeled mice | EECs | 10X Chromium | 1,560 | Not described | (Billing et al., 2019) |
Mus musculus | Colon | Wildtype mice | Epithelium, endothelial and stromal cells | 10X Chromium | 7,395 | GSE151257 | (Brugger et al., 2020) |
Mus musculus | Colon | Wildtype mice | T cells | 10X Chromium | 7,012 | GSE160055 | (Kiner et al., 2021) |
Mus musculus | Colon | DSS-exposed 3Â days | Epithelial and mesenchymal cells | 10X Chromium | 11,495 | GSE156245 | (Wu et al., 2021) |
Mus musculus | Colon | MC38 xenografts upon SHP099 treatment | Cancer cells, stromal cells, and immune cells | 10X Chromium | 7,934(SHP099), 7,881(PBS) | GSE164908 | (Gao et al., 2022) |
Mus musculus | Colon | Wildtype and DSS treated mice | Stromal cells | 10X Chromium | 34,197 | GSE172261 | (Jasso et al., 2022) |
Mus musculus | Distal colon | Wildtype and DSS treated mice | Epithelial, stromal and immune cells | 10X Chromium |  > 35,000 | GSE168033 | (Liu et al., 2022) |
Mus musculus | Colorectal cancer | Primary tumor and lung metastases | Immune cells | 10X Chromium | 12,588 B220+ cells, 3,748 CD38+ cells, 1,588 CD79a+ cells | Not described | (Shen et al., 2021) |
Mus musculus | Small intestine, colon | Wildtype mice | Endothelial cells | 10X Chromium |  > 32,000 | E-MTAB-8077 | (Kalucka et al., 2020) |
Mus musculus | Intestine | pLysDTR mice (DT-treated for 6 consecutive days) | Paneth cells | CEL-seq | 288 | Supplementary dataset S01 | (van Es et al., 2019) |
Mus musculus | Intestine | Wildtype mice | Intestinal stromal cells | Drop-seq | 4,359 | GSE116514 | (Kim et al., 2020) |
Mus musculus | Intestine | Endoderm | Definitive endoderm cells; trophectoderm cells; parietal endoderm cells; visceral endoderm cells; yolk sac endoderm cells | 10X Chromium | 112,217 | GSE123046 | (Nowotschin et al., 2019) |
Mus musculus | Intestine | Embryo of wildtype mice | Epithelial and mesenchymal cells | STRT-seq | 217 | GSE87038 | (Dong et al., 2018) |
Mus musculus | Intestine | Wildtype and irradiated mice | Epithelial cells | 10X Chromium | 2,329 | GSE145866 | (Sheng et al., 2020) |
Mus musculus | Small intestinal organoids | Wildtype and Rfx6 conditional deletion organoids | Epithelial cells | BDâ„¢ Precise WTA Single Cell Kit | 290 | GSE133038 | (Piccand et al., 2019) |
Mus musculus | Small intestinal organoids | Healthy and cancerous organoids | Epithelial cells | Multivariate-barcoded MC |  > 1 million | https://community.cytobank.org/cytobank/login#project-id=1271 | (Qin et al., 2020) |
Mus musculus | Organoids | Lgr5+ cell-derived organoids | EECs | CEL-seq2 | 384 | GSE114988 | (Beumer et al., 2018) |
Mus musculus | Crypts and organoids | Wildtype mice and intestinal organoids | Epithelial cells | CEL-seq | 238 | GSE62270 | (Grun et al., 2015) |
Mus musculus | Neurog3Chrono reporter mice and organoids | Neurog3 labeled mice | EECs | SORT-seq | 6,906 | GSE113561 | (Gehart et al., 2019) |
Mus musculus | Organoids | Lgr5+ and Lgr5− single cells | Epithelial cells | 10X Chromium | 23,421 | GSE115956 | (Serra et al., 2019) |
Mus musculus | Organoids upon RNAi-mediated APC and organoids transplanted into mice | APC mutated cells | Epithelial cells | C1 | 200 | (Ono et al., 2021) | |
Mus musculus | Organoid | Organoids treated with forskolin, CFTRinh-172, or DMSO | Epithelial cells | inDrops | 18,303 | GSE164638 | (Tallapragada et al., 2021) |
Mus musculus | Small intestinal organoids | 5-day differentiated BMP-off and BMP-on organoids | Epithelial cells | SORT-seq | Not described | GSE194004 | (Beumer et al., 2022) |
Mus musculus | Transgene-inducible intestinal organoids | Induced organoids for KRAS, BRAF and CTNNB1 | Epithelial cells | BDâ„¢ Precise WTA Single Cell Kit | 160,000 | GSE115242 | (Brandt et al., 2019) |
Mus musculus | Small intestine and organoids | Wildtype mice and organoids | Epithelial cells | 10X Chromium | 10,180 | GSE100274 | (Mead et al., 2018) |
Mus musculus | Intestinal adenoma of ApcMin/+mice at various time points | Colorectal cancer | Epithelial and mesenchymal cells | 10X Chromium | 79,801 | GSE136256 | (Zowada et al., 2021) |
Homo sapiens | Ileum | CD tissues | Lamina propria cells | 10X Chromium | 82,417 | GSE134809 | (Martin et al., 2019) |
Homo sapiens | Ileum | Health and CD tissues | Immune cells | 10X Chromium | 16,731 | GSE157477 | (Jaeger et al., 2021) |
Homo sapiens | Esophagus, stomach, duodenum | Healthy tissues | Epithelium; immune cells | SORT-seq | Not described | GSE157694/EGAS00001004695 | (Busslinger et al., 2021) |
Homo sapiens | Small intestine | Donor- and recipient-derived cells after transplantation | T cells | 10X Chromium | 974 for scRNA-seq,196 for smart-seq | GSE162687 | (FitzPatrick et al., 2021) |
Homo sapiens | Small intestine | Healthy tissues | Epithelial cells | 10X Chromium | 12,590 | GSE185224 | (Burclaff et al., 2022) |
Homo sapiens | Ileum and ileum-derived organoids | Healthy and viral infected tissues | Epithelial cells | 10X Chromium | 25,482 | GSE171620 | (Triana et al., 2021) |
Homo sapiens | Colon | Healthy and IBD tissues | Epithelial and mesenchymal cells | Smart-seq2 | 11,175 | GSE116222 | (Parikh et al., 2019) |
Homo sapiens | Colon | Healthy and UC tissues | Epithelial cells & mesenchymal cells & immune cells | 10X Chromium | 366,650 | SCP259 | (Smillie et al., 2019) |
Homo sapiens | Colon | Colorectal cancer | Cancer cells, stromal cells, and immune cells | 10X Chromium | 27,927 | GSE188711 | (Guo et al., 2022) |
Homo sapiens | Colon | Colorectal cancer | Immune cells | 10X Chromium | 178,630 | OEP001756 | (Wu et al., 2022) |
Homo sapiens | Colon | Tumors and adjacent tissues | T cells | 10X Chromium | 37,931 | EMTAB-9455 | (Masuda et al., 2022) |
Homo sapiens | Colon | Healthy and UC tissues | Immune cells, stromal cells | 10X Chromium | 29,046 | GSE182270 | (Uzzan et al., 2022) |
Homo sapiens | Colon | Healthy tissues | Macrophages | 10X Chromium | 63,970 | EGAD00001007765/EGAS00001005377 | (Domanska et al., 2022) |
Homo sapiens | Colon and rectum | Familial adenomatous polyposis | Environmental cells (endothelial cells, fibroblasts, macrophages, mast cells, T cells and B cells) and epithelial cells | STRT-Seq (modified) | 8,757 | Not described | (Li et al., 2020) |
Homo sapiens | Large intestine | Children with undifferentiated colitis, Crohn’s disease, and ulcerative colitis | Epithelium, mesenchyme and immune cells | 10X Chromium | 73,165 | GSE121380 | (Huang et al., 2019) |
Homo sapiens | Large intestine | Colorectal cancer | Immune and non-immune cells | 10X Chromium and Smart-seq2 | 43,817 (Hi-seq 4000); 10,468 (Smart-seq2) | GSE146771 | (Zhang et al., 2020a) |
Homo sapiens | Large intestine | Healthy; melanoma with Checkpoint inhibitor-induced colitis; melanoma without Checkpoint inhibitor-induced colitis | Immune cells | 10X Chromium | 51,652 | GSE144469 | (Luoma et al., 2020) |
Homo sapiens | Large intestine | Healthy, CD and UC tissues | CD45+ immune cell | 10X Chromium | 63,314 | PRJCA003980 | (Huang et al., 2021) |
Homo sapiens | Large intestine | Healthy and UC tissues | Immune cells | 10X Chromium | 20,678(UC) 16,678 (Health) | GSE162335 | (Devlin et al., 2021) |
Homo sapiens | Ileum, colon, rectum | Precancerous tissues | Epithelial cells | 10X Chromium | 14,537 | GSE125970 | (Wang et al., 2020b) |
Homo sapiens | Small intestine, large intestine | Fetal digestive tissues | Epithelial and mesenchymal cells | STRT-seq | 5,227 | GSE103239 | (Gao et al., 2018) |
Homo sapiens | Embryonic gastrointestinal tract | Healthy tissues | Epithelial cells | Not described | 5,290 | Supplementary Table 1 and 2 | (Tan et al., 2019) |
Homo sapiens | Human embryonic intestinal tract | Healthy tissues | Epithelial, mesenchymal and immune cells | 10X Chromium | 24,783 | E-MTAB-9489 | (Holloway et al., 2021) |
Homo sapiens | Human embryonic and adult intestinal tract | Healthy tissues | Epithelial, mesenchymal and immune cells | 10X Chromium | 428,000 | E-MTAB-9543, E-MTAB-9536, E-MTAB-9532, E-MTAB-9533 and E-MTAB-10386 | (Elmentaite et al., 2021) |
Homo sapiens | Small intestinal organoids | Crohn’s disease patient-derived tissues | Epithelial cells | C1 | 1,037 | Not described | (Suzuki et al., 2018) |
Homo sapiens | Human pluripotent stem cell-derived intestinal organoids | Organoids | Epithelium, mesenchyme, endothelium, and neurons | 10X Chromium | 13,289 | E-MTAB-9228 | (Holloway et al., 2020) |
Homo sapiens | Intestine and organoids | Intestinal tissues and organoids | EECs | 10X Chromium | 15,283 | GSE146799 | (Beumer et al., 2020) |
Homo sapiens | Cell lines | Colorectal cancer | SW480 cells | 10X Chromium & SORT-seq | 192 | Not described | (Yi et al., 2020) |
Homo sapiens | Cell lines | Control and 5FU-treated colon cancer | 5FU-treated RKO, HCT116, SW480 | Drop-seq | 10,421 | GSE149224 | (Park et al., 2020) |
Homo sapiens | Large intestine and cell lines | Healthy tissues and colorectal cancer | Epithelial cells | C1 | 2,221 | GSE81861 | (Wu et al., 2017) |
Homo sapiens | Primary and metastasis tumor | Colorectal cancer | Spheroids, Tumors, PDXs, PDOs | 10X Chromium and iCELL8 | 26,170 | EGAS00001004064 | (Zowada et al., 2021) |
Homo sapiens | Tumors and adjacent normal tissues | Colorectal cancer | T cells | Smart-seq2 | 8,530 | EGAS00001002791 / GSE108989 | (Zhang et al., 2018) |
Homo sapiens | Embryonic, fetal, childhood/adolescence ileum | Healthy and pediatric Crohn’s disease tissues | Epithelial, mesenchymal and immune cells | 10X Chromium | 74,106 | E-MTAB-8901 | (Elmentaite et al., 2020) |
Homo sapiens | Human embryonic intestinal tract | Healthy tissues | Epithelial, mesenchymal and immune cells | 10X Chromium | 76,592 | GSE158328/GSE158702 | (Fawkner-Corbett et al., 2021) |
Mus musculus; Homo sapiens | Intestine and organoids | Colonic mesenchyme; fibroblast-crypt cocultures; Ptger4-knockout crypt epithelial cells | Epithelial cells and mesenchymal cells | Drop-seq | 5,371 | GSE142431 | (Roulis et al., 2020) |
Mus musculus; Homo sapiens | Colon | Healthy, UC and DSS treated tissues | Epithelial and mesenchymal cells | 10X Chromium | 11,549 | GSE114374 | (Kinchen et al., 2018) |
Mus musculus; Homo sapiens | Human embryonic intestinal tract and mouse colon and colitis | Healthy and DSS treated tissues | Epithelial, mesenchymal and immune cells | 10X Chromium | 22,579 | GSE151257/GSE154007 | (Fazilaty et al., 2021) |
Mus musculus; Homo sapiens | Intestinal organoids | Organoids | Epithelial cells | DisCo | 945 | GSE148093 | (Bues et al., 2022) |
Rhesus macaques | Large intestine | Healthy and during acute graft-versus-host disease tissues | T cells | 10X Chromium | 21,490 | GSE142483 | (Tkachev et al., 2021) |
Zebrafish | Whole intestine | Healthy and DSS treated tissues | Epithelial, mesenchymal and immune cells | 10X Chromium | 30,069 | (Nayar et al., 2021) | |
Swine | Ileum | 6 time points in the swine neonatal period | Epithelial cells | 10X Chromium | 40,186 | GSE162287 | (Meng et al., 2021) |
Drosophila melanogaster | Midgut | Healthy tissues | EECs | 10X Chromium | 4,661 | GSE132274 | (Guo et al., 2019) |