Single cell RNA-seq of adult human neural retina

Experiment ID:ERP111594
Technology:scRNA-Seq
Description:To comprehensively profile cell types in the human retina, we performed single cell RNA-sequencing on 20,009 cells obtained post-mortem from three donors and compiled a reference transcriptome atlas. Using unsupervised clustering analysis, we identified 18 transcriptionally distinct clusters representing all known retinal cells: rod photoreceptors, cone photoreceptors, Muller glia cells, bipolar cells, amacrine cells, retinal ganglion cells, horizontal cells, retinal astrocytes and microglia.
DOI:10.15252/embj.2018100811
Source:ERP111594 ENA
Download:
scRNA-Seq droplet-based processed expression values per cell population in Homo sapiensscRNA-Seq droplet-based H5AD data per cell in Homo sapiens

List of assays

Show

entries

Showing 1 to 20 of 39 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
ERX2860947CL:0000604 retinal rod cellretinal rod cell type BUBERON:0003902 retinal neural layerneural retina, right eyeHsapDv:0000206 80-year-old stage (human)80 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single1625127568917329501027520217025498.5Browse results
ERX2860947CL:0000573 retinal cone cellretinal cone cellUBERON:0003902 retinal neural layerneural retina, right eyeHsapDv:0000206 80-year-old stage (human)80 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single162512756891732950281000102424193Browse results
ERX2860947CL:0002371 somatic cellunspecifiedUBERON:0003902 retinal neural layerneural retina, right eyeHsapDv:0000206 80-year-old stage (human)80 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single16251275689173295017810052223239.5Browse results
ERX2860947CL:0000636 Mueller cellMuller cellUBERON:0003902 retinal neural layerneural retina, right eyeHsapDv:0000206 80-year-old stage (human)80 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single162512756891732950394296112524773Browse results
ERX2860947CL:0000561 amacrine cellamacrine cellUBERON:0003902 retinal neural layerneural retina, right eyeHsapDv:0000206 80-year-old stage (human)80 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single16251275689173295017825876623992Browse results
ERX2860947CL:0000129 microglial cellmicroglial cellUBERON:0003902 retinal neural layerneural retina, right eyeHsapDv:0000206 80-year-old stage (human)80 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single1625127568917329503948224520549.5Browse results
ERX2860947CL:0000748 retinal bipolar neuronretinal bipolar neuron type CUBERON:0003902 retinal neural layerneural retina, right eyeHsapDv:0000206 80-year-old stage (human)80 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single16251275689173295022257281523892Browse results
ERX2860947CL:0000740 retinal ganglion cellretinal ganglion cellUBERON:0003902 retinal neural layerneural retina, right eyeHsapDv:0000206 80-year-old stage (human)80 yearsfemaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single1625127568917329501839611419561.5Browse results
ERX2860948CL:0000636 Mueller cellMuller cellUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single117058175668784530640433162525122Browse results
ERX2860948CL:0002371 somatic cellunspecifiedUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single117058175668784530323527109824164.5Browse results
ERX2860948CL:0000748 retinal bipolar neuronretinal bipolar neuron type DUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single117058175668784530286554106223687Browse results
ERX2860948CL:0000740 retinal ganglion cellretinal ganglion cellUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single11705817566878453022842818123.5Browse results
ERX2860948CL:0000604 retinal rod cellretinal rod cell type CUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single1170581756687845308740950922035Browse results
ERX2860948CL:0000573 retinal cone cellretinal cone cellUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single117058175668784530716569190924391.5Browse results
ERX2860948CL:0000561 amacrine cellamacrine cellUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single117058175668784530297253151424505.5Browse results
ERX2860948CL:0000129 microglial cellmicroglial cellUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single11705817566878453010265358922204Browse results
ERX2860949CL:0002371 somatic cellunspecifiedUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single120987555680812720415130132924480.5Browse results
ERX2860949CL:0000748 retinal bipolar neuronretinal bipolar neuron type DUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single120987555680812720252352104923706.5Browse results
ERX2860949CL:0000636 Mueller cellMuller cellUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single120987555680812720642255157225047Browse results
ERX2860949CL:0000604 retinal rod cellretinal rod cell type BUBERON:0003902 retinal neural layerneural retina, left eyeHsapDv:0000136 42-year-old stage (human)42 yearsmaleNANANAHomo sapiensNA10X Genomics V2Illumina HiSeq 2500THREE_PRIMECELL0single1209875556808127203843459350826546Browse results

Showing 1 to 20 of 39 entries

This website requires cookies, and limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our privacy notice.
Do not show this banner again