Single-cell RNA sequencing of human steady-state immune cells from the lamina propria of colon and matching mesenteric lymph nodes

Experiment ID:ERP115651
Technology:scRNA-Seq
Description:The human colon contains an extensively diverse microbial ecosystem and one of the most numerous communities of immune cells. Studies have highlighted dynamic crosstalk between immune cells and commensals. While studies have demonstrated increasing diversity of microbiota from stomach to stool, whether and how immune cell heterogeneity and microbiota diversity change across the colon is undefined. Furthermore, whether these changes are co-depended in the healthy colon is unknown. Here, tissue samples are collected from caecum, transverse colon, sigmoid colon and mLN of cadaveric donors by the Cambridge Biorepository of Translational Medicine (CBTM). We use single cell RNA sequencing (10X genomics) to assess the dynamics of immune cell populations across the colon and in matching lymph nodes. Associated microbiome 16S sequencing data is available.
DOI:10.1038/s41590-020-0602-z
Source:ERP115651 ENA
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scRNA-Seq droplet-based processed expression values per cell population in Homo sapiensscRNA-Seq droplet-based H5AD data per cell in Homo sapiens

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Library ID
Identifier of the RNA-Seq library
Cell type ID
ID of the cell type of the sample
Cell type name
Name of the cell type of the sample
Cell type author annotation
Free text annotation of cell type as provided by authors
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fractionation
Possible values are: cell, transcripts are extracted from the cell; nuclei, transcripts are extracted from the nucleus.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
ERX3382888CL:0000815 regulatory T cellTregUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single31105536417917323001413884215524956Browse results
ERX3382888CL:0000576 monocyteMonocyteUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single31105536417917323002182916519488.5Browse results
ERX3382888CL:0000798 gamma-delta T cellgd TUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single31105536417917323006009936321150.5Browse results
ERX3382888CL:0000451 dendritic cellcycling DCsUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single31105536417917323002056116419593Browse results
ERX3382888CL:0000235 macrophageMacrophageUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single31105536417917323003093720419864Browse results
ERX3382888CL:0000843 follicular B cellFollicular B cellUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single311055364179173230038135118224.5Browse results
ERX3382888CL:0002465 CD11b-positive dendritic cellcDC2UBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single31105536417917323002962319219773Browse results
ERX3382888CL:0000787 memory B cellB cell memoryUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single311055364179173230039985418215Browse results
ERX3382888CL:0001043 activated CD4-positive, alpha-beta T cell, humanActivated CD4 TUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single31105536417917323001778843223925004Browse results
ERX3382888CL:0000236 B cellB cell IgA PlasmaUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single311055364179173230045553468822255Browse results
ERX3382888CL:0000545 T-helper 1 cellTh1UBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single31105536417917323002111840240425193.5Browse results
ERX3382888CL:0000899 T-helper 17 cellTh17UBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single31105536417917323004232207337125912.5Browse results
ERX3382888CL:0000813 memory T cellTcmUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single3110553641791732300729224132524018Browse results
ERX3382888CL:0000625 CD8-positive, alpha-beta T cellCD8 TUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single3110553641791732300481783119723738.5Browse results
ERX3382888CL:0001065 innate lymphoid cellILCUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single31105536417917323002928124020243Browse results
ERX3382888CL:0002038 T follicular helper cellTfhUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single31105536417917323009002335221490Browse results
ERX3382889CL:0000815 regulatory T cellTregUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single35749054225690074601604813619346.5Browse results
ERX3382889CL:0000576 monocyteMonocyteUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single35749054225690074607501338720807Browse results
ERX3382889CL:0000798 gamma-delta T cellgd TUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single357490542256900746042812485923575Browse results
ERX3382889CL:0000451 dendritic cellcycling DCsUBERON:0001153 caecumcaecumHsapDv:0000241 seventh decade stage (human)60 to 64femaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single357490542256900746015021257021974Browse results

Showing 1 to 20 of 313 entries

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