Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Microfluidics]

Experiment ID:SRP222001
Technology:scRNA-Seq
Description:Here we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the single-cell transcriptomic atlas of the human retina. Using a multi-resolution network-based analysis, we identify all major retinal cell types, and their corresponding gene expression signatures. Overall design: Three replicates of macula and peripheral retinas.
DOI:10.1038/s41467-019-12780-8
Source:SRP222001 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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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
SRX6859234CL:0000748 retinal bipolar neuronBPsUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired544821593503173702724811720343Browse results
SRX6859234CL:0000115 endothelial cellEndoUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired5448215935031737010032017763Browse results
SRX6859234CL:0000745 retina horizontal cellHCsUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired544821593503173702263315819753.5Browse results
SRX6859234CL:0000126 macroglial cellMacrogliaUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired544821593503173702059410219968Browse results
SRX6859234CL:0000129 microglial cellMicrogliaUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired5448215935031737050714718674Browse results
SRX6859234CL:0000740 retinal ganglion cellRGCsUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired5448215935031737000Browse results
SRX6859234CL:0000604 retinal rod cellRodsUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired544821593503173701607912320121.5Browse results
SRX6859234CL:0000561 amacrine cellACsUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired544821593503173708731917800.5Browse results
SRX6859235CL:0000604 retinal rod cellRodsUBERON:0013682 peripheral region of retinaregion of mid-peripheral retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired611830624066721704317222721492.5Browse results
SRX6859235CL:0000740 retinal ganglion cellRGCsUBERON:0013682 peripheral region of retinaregion of mid-peripheral retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired6118306240667217057784718551Browse results
SRX6859235CL:0000129 microglial cellMicrogliaUBERON:0013682 peripheral region of retinaregion of mid-peripheral retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired6118306240667217000Browse results
SRX6859235CL:0000573 retinal cone cellConesUBERON:0013682 peripheral region of retinaregion of mid-peripheral retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired61183062406672170140236418386Browse results
SRX6859235CL:0000748 retinal bipolar neuronBPsUBERON:0013682 peripheral region of retinaregion of mid-peripheral retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired611830624066721703330412420102Browse results
SRX6859235CL:0000561 amacrine cellACsUBERON:0013682 peripheral region of retinaregion of mid-peripheral retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired6118306240667217022602518227.5Browse results
SRX6859235CL:0000126 macroglial cellMacrogliaUBERON:0013682 peripheral region of retinaregion of mid-peripheral retinaHsapDv:0000162 68-year-old stage (human)68 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired611830624066721704648423621249.5Browse results
SRX6859236CL:0000745 retina horizontal cellHCsUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000165 71-year-old stage (human)71 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired7185937836778046039493418130.5Browse results
SRX6859236CL:0000604 retinal rod cellRodsUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000165 71-year-old stage (human)71 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired7185937836778046020871350124267Browse results
SRX6859236CL:0000740 retinal ganglion cellRGCsUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000165 71-year-old stage (human)71 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired7185937836778046069684518837.5Browse results
SRX6859236CL:0000126 macroglial cellMacrogliaUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000165 71-year-old stage (human)71 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired7185937836778046012602739023191.5Browse results
SRX6859236CL:0000115 endothelial cellEndoUBERON:0000053 macula luteamacula in the central retinaHsapDv:0000165 71-year-old stage (human)71 yearsmaleNANANAHomo sapiensNA10X Genomics V3NextSeq 500THREE_PRIMECELL0paired7185937836778046021432218130.5Browse results

Showing 1 to 20 of 50 entries

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