The Fly Cell Atlas: single-cell transcriptomes of the entire adult Drosophila - 10x dataset

Experiment ID:ERP129698
Technology:scRNA-Seq
Description:Single-cell technologies have ushered in a new era for Drosophila research, allowing researchers to obtain transcriptomes for all stable cell types and dynamic cell states. Here we present the first release of the adult Fly Cell Atlas (FCA), which includes 580k cells from 15 individually dissected sexed tissues, as well as from the entire head and body. We annotated more than 250 distinct cell types across all tissues. Few cell types were uniquely detected in the entire head and body samples, suggesting high cell-type saturation. We provide an in-depth analysis of gene signatures and transcription factor combinations, as well as sexual dimorphism, across the whole animal. Finally, we studied cell type lineages that are shared between tissues, such as blood cells and muscle cells, allowing the retrieval of rare cell types and tissue- specific subtypes. This atlas provides a valuable resource for the entire Drosophila community as a reference to study genetic perturbations and disease models at single-cell resolution.
Cell count:313,564
DOI:10.1126/science.abk2432
Source:ERP129698  SRA
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scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogasterscRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster

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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
ERX5671924FBbt:00003730 T neuron T3 (Drosophila)T neuron T3UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993001158840Browse results
ERX5671924FBbt:00003741 lamina wide-field cell (Drosophila)lamina wide-field 1 neuronUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired63041068257730599300698264.5Browse results
ERX5671924FBbt:00003743 centrifugal neuron C2 (Drosophila)centrifugal neuron C2UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993001048644Browse results
ERX5671924FBbt:00003744 centrifugal neuron C3 (Drosophila)centrifugal neuron C3UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993001359036.5Browse results
ERX5671924FBbt:00003770 distal medullary amacrine neuron Dm3 (Drosophila)distal medullary amacrine neuron Dm3UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired63041068257730599300638265Browse results
ERX5671924FBbt:00003776 medullary intrinsic neuron Mi1 (Drosophila)medullary intrinsic neuron Mi1UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993002579873Browse results
ERX5671924FBbt:00003779 medullary intrinsic neuron Mi4 (Drosophila)medullary intrinsic neuron Mi4UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993001238980.5Browse results
ERX5671924FBbt:00003784 medullary intrinsic neuron Mi9 (Drosophila)medullary intrinsic neuron Mi9UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired63041068257730599300738449.5Browse results
ERX5671924FBbt:00003789 transmedullary neuron Tm1 (Drosophila)transmedullary neuron Tm1UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993001959576Browse results
ERX5671924FBbt:00003790 transmedullary neuron Tm2 (Drosophila)transmedullary neuron Tm2UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993001399089Browse results
ERX5671924FBbt:00003791 transmedullary neuron Tm3a (Drosophila)transmedullary neuron Tm3aUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993001259008Browse results
ERX5671924FBbt:00003792 transmedullary neuron Tm4 (Drosophila)transmedullary neuron Tm4UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993001499130Browse results
ERX5671924FBbt:00003797 transmedullary neuron Tm9 (Drosophila)transmedullary neuron Tm9UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired63041068257730599300638280.5Browse results
ERX5671924FBbt:00003808 transmedullary neuron Tm20 (Drosophila)transmedullary neuron Tm20UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired63041068257730599300728474.5Browse results
ERX5671924FBbt:00003821 transmedullary Y neuron TmY4 (Drosophila)transmedullary Y neuron TmY4UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired63041068257730599300508041.5Browse results
ERX5671924FBbt:00003823 transmedullary Y neuron TmY5a (Drosophila)transmedullary Y neuron TmY5aUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993001279051.5Browse results
ERX5671924FBbt:00003826 transmedullary Y neuron TmY8 (Drosophila)transmedullary Y neuron TmY8UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired63041068257730599300938642Browse results
ERX5671924FBbt:00003835 proximal medullary amacrine neuron Pm2 (Drosophila)proximal medullary amacrine neuron Pm2UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired63041068257730599300758293Browse results
ERX5671924FBbt:00004225 photoreceptor cell R7 (Drosophila)photoreceptor cell R7UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993001509059.5Browse results
ERX5671924FBbt:00004227 photoreceptor cell R8 (Drosophila)photoreceptor cell R8UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5malew1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired630410682577305993002219693.5Browse results

Showing 81 to 100 of 1518 entries