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
Download:
scRNA-Seq droplet-based processed expression values per cell population in Drosophila melanogasterscRNA-Seq droplet-based H5AD data per cell in Drosophila melanogaster

List of assays

Show

entries

Showing 1 to 20 of 1518 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
ERX5671923CL:0000066 epithelial cellepithelial cellUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired114955742410817927920048111391Browse results
ERX5671923CL:0000387 hemocyte (sensu Nematoda and Protostomia)hemocyteUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired1149557424108179279200738297Browse results
ERX5671923CL:0000565 fat body cellNAUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792001779463Browse results
ERX5671923CL:0000700 dopaminergic neurondopaminergic neuronUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired1149557424108179279200908410.5Browse results
ERX5671923CL:0000718 compound eye cone cellcone cellUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired114955742410817927920060211551.5Browse results
ERX5671923CL:0001658 visual pigment cell (sensu Nematoda and Protostomia)pigment cellUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792001809744.5Browse results
ERX5671923CL:0008004 somatic muscle cellskeletal muscle of headUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792002009712Browse results
ERX5671923FBbt:00001258 subperineurial glial cell (Drosophila)subperineurial glial cellUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired1149557424108179279200598538.5Browse results
ERX5671923FBbt:00003686 Kenyon cell (Drosophila)Kenyon cellUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792001548911Browse results
ERX5671923FBbt:00003719 lamina monopolar neuron L1 (Drosophila)lamina monopolar neuron L1UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792002479578Browse results
ERX5671923FBbt:00003720 lamina monopolar neuron L2 (Drosophila)lamina monopolar neuron L2UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792003169842Browse results
ERX5671923FBbt:00003721 lamina monopolar neuron L3 (Drosophila)lamina monopolar neuron L3UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792002319729.5Browse results
ERX5671923FBbt:00003722 lamina monopolar neuron L4 (Drosophila)lamina monopolar neuron L4UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792001729200.5Browse results
ERX5671923FBbt:00003725 lamina monopolar neuron L5 (Drosophila)lamina monopolar neuron L5UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792001479066Browse results
ERX5671923FBbt:00003727 columnar neuron T1 (Drosophila)columnar neuron T1UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792002449623.5Browse results
ERX5671923FBbt:00003728 T neuron T2 (Drosophila)T neuron T2UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792001619333Browse results
ERX5671923FBbt:00003729 T neuron T2a (Drosophila)T neuron T2aUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792001749497.5Browse results
ERX5671923FBbt:00003730 T neuron T3 (Drosophila)T neuron T3UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792001699444.5Browse results
ERX5671923FBbt:00003741 lamina wide-field cell (Drosophila)lamina wide-field 1 neuronUBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired1149557424108179279200547975.5Browse results
ERX5671923FBbt:00003743 centrifugal neuron C2 (Drosophila)centrifugal neuron C2UBERON:6000004 insect headheadFBdv:00007080 day 5 of adulthood (fruit fly)5mixedw1118NANADrosophila melanogasterNA10X Genomics V3Illumina NovaSeq 6000THREE_PRIMENUCLEUS0paired11495574241081792792002079614Browse results

Showing 1 to 20 of 1518 entries