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
ERX9138748CL:0002063 type II pneumocyteAT2, EpitheliaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single15261784589953327033707799023459Browse results
ERX9138748CL:0000583 alveolar macrophageMacro_alveolar, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1526178458995332701636915319015.5Browse results
ERX9138748CL:0000192 smooth muscle cellMuscle_smooth_pulmonary, StromaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single15261784589953327068807718410Browse results
ERX9138748CL:1001603 lung macrophageMacro_CHIT1, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single15261784589953327012892517852.5Browse results
ERX9138748CL:1001568 pulmonary artery endothelial cellEndothelia_vascular_arterial_pulmonary, VascularUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single15261784589953327060496118482Browse results
ERX9138748CL:0002543 vein endothelial cellEndothelia_vascular_venous_pulmonary, VascularUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1526178458995332701800715419155Browse results
ERX9138748CL:0002553 fibroblast of lungFibro_adventitial, StromaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single15261784589953327019612673822174.5Browse results
ERX9138748CL:0000623 natural killer cellNK_CD16hi, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single15261784589953327058496518422Browse results
ERX9138748CL:0000160 goblet cellSecretory_Goblet, EpitheliaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1526178458995332708182117769Browse results
ERX9138748CL:0000158 club cellSecretory_Club, EpitheliaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single15261784589953327023253417938Browse results
ERX9138748CL:0000897 CD4-positive, alpha-beta memory T cellCD4_TRM, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single15261784589953327012632017803.5Browse results
ERX9138748CL:0000990 conventional dendritic cellDC_2, ImmuneUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single15261784589953327057847518248.5Browse results
ERX9138748CL:0000067 ciliated epithelial cellCiliated, EpitheliaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1526178458995332706325945121440Browse results
ERX9138748CL:0002144 capillary endothelial cellEndothelia_vascular_Cap_g, VascularUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1526178458995332701143110918795.5Browse results
ERX9138748CL:0009115 lymph node lymphatic vessel endothelial cellEndothelia_Lymphatic, VascularUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1526178458995332709935455021567.5Browse results
ERX9138748CL:1000413 endothelial cell of arteryEndothelia_vascular_arterial_systemic, VascularUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1526178458995332708762217742Browse results
ERX9138748CL:0002062 type I pneumocyteAT1 , EpitheliaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single1526178458995332709863148321765.5Browse results
ERX9138748CL:0000186 myofibroblast cellFibro_myofibroblast, StromaUBERON:0008953 lower lobe of left lungLower Left LobeHsapDv:0000123 29-year-old stage (human)25-30 (29 in HCA)maleWhiteNANAHomo sapiensNA10X Genomics V2Illumina HiSeq 4000THREE_PRIMECELL0single15261784589953327033334318135.5Browse results
ERX9138751CL:0002144 capillary endothelial cellEndothelia_vascular_Cap_a, 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_PRIMECELL0single171499603108600695064910592924335.5Browse results
ERX9138751CL:0000583 alveolar macrophageMacro_alveolar, 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_PRIMECELL0single1714996031086006950722840133523975Browse results

Showing 1 to 20 of 1208 entries

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