A human breast transcriptome atlas

Experiment ID:SRP329970
Technology:scRNA-Seq
Description:The breast is a dynamic organ whose response to physiological and pathophysiological conditions alters its disease susceptibility, yet the specific effects of these clinical variables on cell state remain poorly annotated. We present a unified, high-resolution breast atlas by integrating single-cell RNA-seq, mass cytometry, and cyclic immunofluorescence, encompassing a myriad of states. We define cell subtypes within the alveolar, hormone-sensing, and basal epithelial lineages, delineating associations of several subtypes with cancer risk factors, including age, parity, and BRCA2 germline mutation. Of particular interest is a subset of alveolar cells termed basal-luminal (BL) cells, which exhibit poor transcriptional lineage fidelity, accumulate with age, and carry a gene signature associated with basal-like breast cancer. We further utilize a medium-depletion approach to identify molecular factors regulating cell-subtype proportion in organoids. Together, these data are a rich resource to elucidate diverse mammary cell states. Overall design: A total of 16 breast samples were assayed (4 samples from reductive mammoplasties and 12 from prophylactic mastectomies).
DOI:10.1016/j.devcel.2022.05.003
Source:SRP329970 SRA
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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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Showing 1 to 20 of 36 entries

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
SRX11559742CL:0000183 contractile cellVL3_PEUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired37882521827529247301185930130824696.5Browse results
SRX11559742CL:0002325 mammary alveolar cellAPUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired37882521827529247305172621328826106Browse results
SRX11559742CL:0002555 fibroblast of mammary glandF_doubletsUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired3788252182752924730668374125924360Browse results
SRX11559742CL:0002324 myoepithelial cell of mammary glandBA_doubletsUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired37882521827529247302907822919662.5Browse results
SRX11559742CL:2000071 mammary microvascular endothelial cellVL2_VEUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired37882521827529247307194501351326365.5Browse results
SRX11559742CL:0000786 plasma cellI5_PlasmaCellUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired3788252182752924730121720763122381.5Browse results
SRX11559742CL:0002326 luminal epithelial cell of mammary glandHSaUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired37882521827529247301331584199524771Browse results
SRX11559742CL:0000763 myeloid cellI1_MyeloidUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired3788252182752924730928894119724271Browse results
SRX11559742CL:0000623 natural killer cellI2_NKUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired37882521827529247307255328721101Browse results
SRX11559742CL:0000084 T cellI3_TcellUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired378825218275292473081324190124016.5Browse results
SRX11559742CL:0000236 B cellI4_BcellUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired37882521827529247301888714519056.5Browse results
SRX11559742CL:0002138 endothelial cell of lymphatic vesselVL1_LEUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000135 41-year-old stage (human)41femaleWhiteNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired378825218275292473013799346121854.5Browse results
SRX11559756CL:0000786 plasma cellI5_PlasmaCellUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000130 36-year-old stage (human)36femaleBlackNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired248596145179224150074824345721608.5Browse results
SRX11559756CL:0002555 fibroblast of mammary glandF_doubletsUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000130 36-year-old stage (human)36femaleBlackNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired2485961451792241500879865140324714.5Browse results
SRX11559756CL:0002324 myoepithelial cell of mammary glandBA_doubletsUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000130 36-year-old stage (human)36femaleBlackNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired248596145179224150030665273123106Browse results
SRX11559756CL:0000183 contractile cellVL3_PEUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000130 36-year-old stage (human)36femaleBlackNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired248596145179224150016947343822188.5Browse results
SRX11559756CL:2000071 mammary microvascular endothelial cellVL2_VEUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000130 36-year-old stage (human)36femaleBlackNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired2485961451792241500625181103623768.5Browse results
SRX11559756CL:0002138 endothelial cell of lymphatic vesselVL1_LEUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000130 36-year-old stage (human)36femaleBlackNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired248596145179224150016731353722274Browse results
SRX11559756CL:0000084 T cellI3_TcellUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000130 36-year-old stage (human)36femaleBlackNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired248596145179224150018205843422012Browse results
SRX11559756CL:0000236 B cellI4_BcellUBERON:0005200 thoracic mammary glandMammary tissueHsapDv:0000130 36-year-old stage (human)36femaleBlackNANAHomo sapiensNA10X Genomics V2HiSeq X TenTHREE_PRIMECELL0paired24859614517922415003410017819552Browse results

Showing 1 to 20 of 36 entries

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