by Teichlab
Wellcome Sanger Institute
Part of Human Cell Atlas
Space-Time Gut Cell Atlas

Full single cell RNA-seq dataset of 428K intestinal cells from fetal, pediatric, adult donors, and up to 11 intestinal regions. Click here to access the preprint.

Explore the cell type lineages below
Fetal and Pediatric Cell Atlas
Single-cell transcriptomes for 62,849 cells isolated from 6-11 weeks post-conception developing human gut. This data includes intestinal cells from duo-jejunum, ileum and colon.
Single-cell transcriptomes isolated from terminal ileum of childhood onset Crohn’s disease and matched healthy controls. This map includes total of 22,500 cells from 8 control samples and 7 Chron’s disease samples.
Human fetal epithelium

Human fetal epithelium architecture before crypt-villus emergence.

Intestinal stem cells

Emergence of intestinal stem cells (green, LGR5) in the human fetal intestine.

Human enteric nervous system

Human enteric nervous system development. Colonisation of the myenteric plexus by enteric neural progenitors.

Gut immune system development

Gut immune system development. Surveilance by lymphoid tissue initiator (LTi) cells.

Histology & RNAscope imaging by the Cellular Generation and
Phenotyping (CGaP)
core facility and Bayraktar Lab.
Colon Immune Atlas

The colon, as a barrier tissue, represents a unique immune environment where immune cells display tolerance toward adiverse community of microbes, which are collectively known as the microbiome.

Colon Schematic Thepublished study  revealed that not only were there differences between the immune cells in different parts of the colon, but that the microbiome also subtly changed, with a broader range of bacteria further down the colon.

Image description Single cell transcriptomes for 41,650 cells isolated from the caeacum, transverse colon and sigmoid colon of 5 individuals.

Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease
Elmentaite R, Ross A D B, Roberts K, James K R, Ortmann D, Gomes T, Nayak K, Tuck L, Pritchard S, Bayraktar O A, Heuschkel R, Vallier L, Teichmann S A, Zilbauer M.
2020 Dec 21
Distinct microbial and immune niches of the human colon
James K R, Gomes T, Elmentaite R, Kumar N, Gulliver E L, King H W, Stares M D, Bareham B R, Ferdinand J R, Petrova V N, Polański K, Forster S C, Jarvis L B, Suchanek O, Howlett S, James L K, Jones J L, Meyer K B, Clatworthy M R, Saeb-Parsy K, Lawley T D, Teichmann S A.
2020 Feb 17
Sarah Teichmann
Sarah Teichmann

Wellcome Sanger Institute &
University of Cambridge

Matthias Zilbauer
Matthias Zilbauer

University Lecturer and
Hon. Consultant
Department of Paediatrics
University of Cambridge

Kylie James
Kylie James

Group Leader
Garvan Institute, Sydney

Rasa Elmentaite
Rasa Elmentaite

PhD candidate
Wellcome Sanger Institute

Alexander Ross
Alexander Ross

NIHR Academic Clinical
Fellow and Honorary
Specialty Registrar
in Medical Genetics
University of Cambridge

Collaborating Groups