Single-Cell

Single-Cell RNA Sequencing Datasets with Circadian Analysis

Available Datasets

Dataset Name Species Tissue Timepoints Technology GSE Link Paper Atlas # Cell Types Downloads
Mouse SCN Cells
Single-cell RNA sequencing of mouse SCN cells to study circadian organization. 		Mus musculus Suprachiasmatic nucleus [14, 18, 22, 26, 30, 34, 38, 42, 46, 50, 54, 58] Drop-seq GSE Paper Link 7
BIO_CYCLE.zip annotated/gse117295_scn_annotated.h5ad
Mouse Liver Clock
Single-cell RNA sequencing of mouse liver hepatocytes across the circadian cycle. 		Mus musculus Liver [0, 6, 12, 18] 10x Genomics GSE Paper N/A 1
BIO_CYCLE.zip
Fly Clock Constant Darkness
Single-cell profiling of Drosophila clock neurons under constant darkness conditions. 		Drosophila melanogaster Brain [2, 6, 10, 14, 18, 22] CEL-seq2 GSE Paper Link 17
BIO_CYCLE.zip annotated/gse157504_clock_neurons_annotated.h5ad
Fly clock Light-Dark
Single-cell profiling of Drosophila clock neurons under light dark conditions. 		Drosophila melanogaster Brain [2, 6, 10, 14, 18, 22] CEL-seq2 GSE Paper Link 17
BIO_CYCLE.zip annotated/gse157504_clock_neurons_annotated.h5ad
Fly Clock Dopamine
Single-cell analysis of Drosophila clock and dopaminergic neurons. 		Drosophila melanogaster Brain [2, 6, 10, 14, 18, 22] CEL-seq2 GSE Paper Link 17
BIO_CYCLE.zip annotated/gse198948_clock_neurons_annotated.h5ad
Fly Clock GPCR
Single-cell sequencing of Drosophila clock neurons enriched for GPCR signaling. 		Drosophila melanogaster Brain [2, 14] Smart-seq2 GSE Paper N/A 2
BIO_CYCLE.zip
Mouse Aorta Light-Dark
Single-cell sequencing of male mouse aorta collected over the light-dark cycle. 		Mus musculus Whole Aorta [0, 6, 12, 18] 10x Genomics GSE Paper N/A 4
BIO_CYCLE.zip
Human Heart ACR
Single-nucleus RNA sequencing of human heart tissue with abnormal circadian rhythm (ACR). 		Homo sapiens Heart (left ventricle) [8, 16] 10x Genomics GSE Paper Link 17
BIO_CYCLE.zip annotated/gse270258_annotated.h5ad
Human Heart NCR
Single-nucleus RNA sequencing of human heart tissue with normal circadian rhythm (NCR). 		Homo sapiens Heart (left ventricle) [8, 16] 10x Genomics GSE Paper Link 17
BIO_CYCLE.zip annotated/gse270258_annotated.h5ad
Mouse Skin
Single-cell RNA sequencing of mouse skin across the circadian cycle. 		Mus musculus Dorsal Dermis [2, 6, 10, 14, 22, 26, 30, 34, 38, 42, 46, 50, 54, 58, 62, 66, 70] 10x Genomics GSE Paper Link 5
BIO_CYCLE.zip annotated/gse223109_skin_annotated.h5ad
Mouse PVN
Single-nucleus RNA sequencing of mouse Paraventricular Nucleus (PVN) during day and night. 		Mus musculus Hypothalamus PVN [8, 20] 10x Genomics GSE Paper Link 6
BIO_CYCLE.zip annotated/gse231734_pvn_annotated.h5ad
Fly DN3 ClockNeurons
Single-cell RNA sequencing of Drosophila DN3 clock neurons. 		Drosophila melanogaster Brain [2, 6, 10, 14, 18, 22] 10x Genomics GSE Paper Link 17
BIO_CYCLE.zip annotated/gse276175_clock_neurons_annotated.h5ad
Mouse Muscle
Single-cell analysis of mouse muscle regeneration under circadian control. 		Mus musculus Skeletal muscle [4, 16, 28, 40, 76, 88] 10x Genomics GSE Paper Link 9
BIO_CYCLE.zip annotated/muscle_with_celltypes_gpu.h5ad
Mouse Tongue
Single-cell RNA sequencing of mouse taste epithelium across day and night. 		Mus musculus Tongue epithelium [0, 12] 10x Genomics GSE Paper Link 8
BIO_CYCLE.zip annotated/scn_with_celltypes_gpu.h5ad
Mouse Liver Multiome
Single-nucleus multiomic profiling of mouse liver across circadian time. 		Mus musculus Liver [2, 6, 10, 14, 18, 22] 10x Genomics N/A Paper N/A 4
BIO_CYCLE.zip

Interactive Gene Expression Analysis

Gene Oscillation Plot