Spatiotemporal single cell transcriptomic analysis of human gut macrophages reveals multiple functional and niche-specific subsets

1 Dataset 3 Publications

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Dataset ID	Description	Technology	Samples
EGAD00001007765	Cellular suspensions (∼15000 cells, with expected recovery of ∼7500 cells) of sorted CD45+ HLA-DR+ CD14+ macrophages from colonic mucosa and muscularis propria were loaded on the 10X Chromium Controller instrument (10X Genomics) according to the manufacturer’s protocol using the 10X GEMCode proprietary technology. All samples from individual patients were loaded in one batch. The Chromium Single Cell 3´ v2 Reagent kit (10X Genomics) was used to generate the cDNA and prepare the libraries, according to the manufacturer’s protocol. The libraries were then equimolarly pooled and sequenced on an Illumina NextSeq500 using HighOutput flow cells v2.5. A coverage of 400M reads per sample was targeted, in order to obtain 50 000 reads per cell. The raw data were then demultiplexed and processed with the Cell Ranger software (10X Genomics) v2.1.1.	NextSeq 500	8

Publications	Citations
Single-cell transcriptomic analysis of human colonic macrophages reveals niche-specific subsets. Domanska D, Majid U, Karlsen VT, Merok MA, Beitnes AR, Yaqub S, Bækkevold ES, Jahnsen FL. J Exp Med 219: 2022 e20211846	25
Intestinal cellular heterogeneity and disease development revealed by single-cell technology. Wang Y, Song W, Yu S, Liu Y, Chen YG. Cell Regen 11: 2022 26	8
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis. Umu SU, Rapp Vander-Elst K, Karlsen VT, Chouliara M, Bækkevold ES, Jahnsen FL, Domanska D. Gigascience 12: 2022 giad091	5