Transcriptomics

Dataset Information

11

ScRNA-seq of pluripotent stem cell derived human intestinal organoids, adult intestine, and human fetal endoderm derived organs


ABSTRACT: Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human definitive endoderm and intestinal organoids (HIOs) at several timepoints of in vitro growth (7, 14, and 28 days) and after in vivo growth beneath the kidney capsule of a murine host (4 and 8 wks post-transplant). Additionally, we profiled HIOs grown in a non-adhesive alginate hydrogel and also CDX2 knockout HIOs. In order to benchmark the organoid cultures, we used scRNA-seq to profile primary human fetal esophagus (14.3 pcw, 16.7 pcw), stomach (6.7, 14.3, and 16.7 pcw), liver (14.4 pcw), small intestine ( 11.4 and 14.4 pcw) and colon (11.4, 14.4, and 18.9 pcw). Diverse cell lineages were captured across all tissues profiled, including: epithelium, mesenchyme, neurons, endothelium, and immune lineages.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens  

DISEASE(S): Normal

SUBMITTER: Qianhui Yu   Jason R Spence   Emily M Holloway   Joshua H Wu  

PROVIDER: E-MTAB-10187 | ArrayExpress | 2021-05-21

SECONDARY ACCESSION(S): ERP127429

REPOSITORIES: ArrayExpress, ENA

Dataset's files

Source:
Action DRS
1-HIO-Fresh_S1_L001_I1_001.fastq.gz Fastqsanger.gz
1-HIO-Fresh_S1_L001_R1_001.fastq.gz Fastqsanger.gz
1-HIO-Fresh_S1_L001_R2_001.fastq.gz Fastqsanger.gz
1-HIO-Fresh_S1_L002_I1_001.fastq.gz Fastqsanger.gz
1-HIO-Fresh_S1_L002_R1_001.fastq.gz Fastqsanger.gz
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