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

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

PROVIDER: PRJEB45570 | ENA |

REPOSITORIES: ENA

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

Project 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.

2021-07-01 | E-MTAB-10519 | biostudies-arrayexpress

Fly Cell Atlas: single-cell transcriptomes of the entire adult Drosophila - Smartseq2 dataset

Project description:Fly Cell Atlas: single-cell transcriptomes of the entire adult Drosophila - Smartseq2 dataset

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Fly Cell Atlas: single-cell transcriptomes of the entire adult Drosophila - Smartseq2 dataset

Project description:We have been performing single-cell RNAseq profiling for the entire adult Drosophila. Here we are providing raw data generated from the Smart-seq2 platform. They are from 37 384-well plates.

2021-09-21 | E-MTAB-10628 | biostudies-arrayexpress

Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution

Project description:Aging is accompanied by the functional decline of all tissues, but it is still largely unknown how aging impacts different tissues in a cell type-specific manner. Here, we present the Aging Fly Cell Atlas (AFCA) that includes single-nucleus transcriptomes of the entire Drosophila head and body from both males and females at four different ages. We characterize 162 distinct cell types and present an in-depth analysis of cell type-specific aging features, including changes of cell composition, gene expression, number of expressed genes, transcriptome noise, and cell identity. By combining all aging features, including aging clock models predicting a cell’s age, we find cell-type specific aging patterns. Adipose tissues showed the highest aging score, followed by two cell types from the reproductive system. This transcriptomic atlas provides a valuable resource for the community to study fundamental principles of aging in complex organisms.

2022-12-06 | GSE218661 | GEO

Differentiation of entire complement of spinal sensory interneurons from mouse embryonic stem cells (mESCs) [10X]

Project description:Differentiation of entire complement of spinal sensory interneurons from mouse embryonic stem cells (mESCs) [10X]

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Chicken genome assembly validation using Chromium 10x linked-read sequencing dataset.

Project description:Chicken genome assembly validation using Chromium 10x linked-read sequencing dataset.

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scRNA-seq of first and second trimester human gonads - 10x dataset

Project description:scRNA-seq of first and second trimester human gonads - 10x dataset

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Adult rat ventral tegmental area single-nucleus RNA-seq dataset for "An atlas of transcriptionally defined cell populations in the rat ventral tegmental area"

Project description:This dataset contains single-nucleus RNA sequencing results from adult rat brain (ventral tegmenal area, or VTA). The goal of this experiment was to define the transcriptional landscapes of distinct cell types in the VTA. Single-cell sequencing was carried out with nuclei suspensions (sorted using flow cytometry) using the 10X Genomics Chromium single cell sequencing platform.

2021-03-31 | GSE168156 | GEO

Identification of genes regulated by Fer2 in the fly brain using an overexpression approach

Project description:The transcription factor Fer2 plays a neuroprotective role in the dopaminergic neurons of the fly brain, but the underlying molecular mechanisms are not understood. By performing RNA-seq on fly heads after Fer2 inducible overexpression, we identified hundreds of genes differentially regulated in response to Fer2 overexpression. Combining this dataset with Fer2 ChIP-seq on the fly head, we obtained a list of 26 direct target genes, bound and regulated by Fer2.

2020-08-27 | GSE156890 | GEO

Genome-wide map of the binding sites of the transcription factor Fer2 in the fly brain

Project description:The transcription factor Fer2 plays a neuroprotective role in the dopaminergic neurons of the fly brain, but the underlying molecular mechanisms are not understood. By using chromatin immunoprecipitation coupled to sequecing (ChIP-seq), we identified over 250 genomic binding sites bound by Fer2 in the fly brain. Combining this dataset with RNA-seq of fly heads upon inducible Fer2 overexpression, we obtained a list of 26 direct target genes, bound and regulated by Fer2.

2020-08-27 | GSE156892 | GEO

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