scRNAseq from pbmc, ileum, and rectal tissue of healthy and crohns disease individuals

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA938415 and SRA study SRP433396. Searching any of these in the dataset finder brings you back here.

Supports a case/control comparison: 25 samples read as cases, 21 as controls.

How we read this: Read from 46 sample titles: 46 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

• GSM7061852 Disease Ileum 57 yo F
• GSM7061853 Disease PBMC 57 yo F
• GSM7061854 Disease Rectum 57 yo F
• GSM7061855 Disease Ileum 40 yo M
• GSM7061856 Disease PBMC 40 yo M
• GSM7061857 Disease Rectum 40 yo M
• GSM7061858 Disease Ileum 41 yo M
• GSM7061859 Disease PBMC 41 yo M
• GSM7061860 Disease Rectum 41 yo M
• GSM7061861 Disease Ileum 26 yo F [CD8]
• GSM7061862 Disease PBMC 26 yo F [CD8]
• GSM7061863 Disease Rectum 26 yo F
• GSM7061864 Disease PBMC 55 yo M
• GSM7061865 Disease Rectum 55 yo M
• GSM7061866 Disease Ileum 26 yo F [CD10]
• GSM7061867 Disease Rectum 26 yo F [CD10]
• GSM7061868 Disease Ileum 74 yo F
• GSM7061869 Disease PBMC 74 yo F
• GSM7061870 Disease Rectum 74 yo F
• GSM7061871 Disease Ileum 39 yo M
• GSM7061872 Disease PBMC 39 yo M
• GSM7061873 Disease Rectum 39 yo M
• GSM7061874 Disease Ileum 72 yo M
• GSM7061875 Disease PBMC 72 yo M
• GSM7061876 Disease Rectum 72 yo M
• GSM7061877 Healthy Ileum 36 yo M
• GSM7061878 Healthy PBMC 36 yo M
• GSM7061879 Healthy Rectum 36 yo M
• GSM7061880 Healthy Ileum 33 yo F
• GSM7061881 Healthy PBMC 33 yo F
• GSM7061882 Healthy Rectum 33 yo F
• GSM7061883 Healthy Ileum 23 yo M
• GSM7061884 Healthy PBMC 23 yo M
• GSM7061885 Healthy Rectum 23 yo M
• GSM7061886 Healthy Ileum 59 yo F
• GSM7061887 Healthy PBMC 59 yo F
• GSM7061888 Healthy Rectum 59 yo F
• GSM7061889 Healthy Ileum 61 yo M
• GSM7061890 Healthy PBMC 61 yo M
• GSM7061891 Healthy Rectum 61 yo M

+ 6 more — browse all 46 samples with per-sample file links →

• GSE267718 Single cell RNA sequencing (scRNAseq) of urine-derived cells, peripheral blood mononuclear (PBMC), and tumor cells from bladder cancer patients. 33 samples shares scrnaseq, pbmc
• GSE266852 Comparison of differential gene expression in blood PBMCs from healthy controls, patients with rheumatoid arthritis,and patients with lupus using single-cell transcriptome sequencing analysis. 10 samples shares healthy, pbmc
• GSE36701 Gene expression analysis of rectal mucosa in chronic irritable bowel syndrome (IBS) compared to healthy volunteers (HV) 221 samples shares healthy, rectal
• GSE294559 Single-cell multi-omics characterize colorectal tumors, adjacent healthy tissue and matched organoids identifying CRC-unique features 72 samples shares healthy, rectal
• GSE268210 Single-cell analysis of human PBMCs in healthy and type 2 diabetes populations: Dysregulated immune networks in type 2 diabetes unveiled through single-cell profiling 30 samples shares healthy, pbmc
• GSE281106 Single-cell RNA-seq of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases [scRNAseq_KR_SGI] 352 samples shares scrnaseq
• GSE325391 Unique transcriptional profiles of adult human immature neurons in healthy aging, Alzheimer’s disease, and cognitive resilience 27 samples shares healthy
• GSE256491 Single-cell atlas of the human brain vasculature across development, adulthood and disease (Extra Individuals) 16 samples shares individuals

Search all human RNA-seq datasets in GEO →