A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche

Experiment ID:ERP136992
Technology:scRNA-Seq
Description:Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).
DOI:10.1038/s41588-022-01243-4
Source:ERP136992 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
ERX9138755CL:0000990 conventional dendritic cellDC_1, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17361332911567941101839415518911.5Browse results
ERX9138755CL:0002543 vein endothelial cellEndothelia_vascular_venous_pulmonary, VascularUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411039356580623612.5Browse results
ERX9138755CL:0000624 CD4-positive, alpha-beta T cellCD4_EM/Effector, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17361332911567941106564328421421.5Browse results
ERX9138755CL:0000057 fibroblastNAF_endoneurial, StromaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411080518118731.5Browse results
ERX9138755CL:0002553 fibroblast of lungFibro_adventitial, StromaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1736133291156794110900651136424984Browse results
ERX9138755CL:0000192 smooth muscle cellMuscle_smooth_pulmonary, StromaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411053614388624162.5Browse results
ERX9138755CL:0000913 effector memory CD8-positive, alpha-beta T cellCD8_EM, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17361332911567941101174411719066Browse results
ERX9138755CL:0002633 respiratory basal cellBasal, EpitheliaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411016610459723061.5Browse results
ERX9138755CL:0001054 CD14-positive monocyteMonocyte_CD14, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411016051717893.5Browse results
ERX9138755CL:0000909 CD8-positive, alpha-beta memory T cellCD8_TRM, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411017572417988.5Browse results
ERX9138755CL:0002396 CD14-low, CD16-positive monocyteMonocyte_CD16, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411066487018455.5Browse results
ERX9138755CL:0000186 myofibroblast cellFibro_myofibroblast, StromaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411010495737222388Browse results
ERX9138755CL:0000235 macrophageMacro_AW_CX3CR1, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411018072717949Browse results
ERX9138755CL:0000623 natural killer cellNK_CD11d, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17361332911567941109171617842Browse results
ERX9138755CL:1001603 lung macrophageMacro_CHIT1, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411000Browse results
ERX9138755CL:0000897 CD4-positive, alpha-beta memory T cellCD4_TRM, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411021692617975.5Browse results
ERX9138755CL:0000077 mesothelial cellMesothelia, StromaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411033633018252.5Browse results
ERX9138755CL:0000097 mast cellMast_cell , ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411046054918334Browse results
ERX9138755CL:1000413 endothelial cell of arteryEndothelia_vascular_arterial_systemic, VascularUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single17361332911567941101570811019631.5Browse results
ERX9138755CL:0000940 mucosal invariant T cellMAIT, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000169 75-year-old stage (human)75-80 (75 in HCA)femaleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single173613329115679411018183217973Browse results

Showing 61 to 80 of 1208 entries

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