Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A multi-omics atlas of the human retina at single-cell resolution

ABSTRACT: A multi-omics atlas of the human retina at single-cell resolution

PROVIDER: PRJNA938514 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23617400_1.fastq.gz	Fastqsanger.gz
	SRR23617400_2.fastq.gz	Fastqsanger.gz
	SRR23617401_1.fastq.gz	Fastqsanger.gz
	SRR23617401_2.fastq.gz	Fastqsanger.gz
	SRR23617402_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 202

Similar Datasets

A multi-omics atlas of the human retina at single-cell resolution

Project description:Cell types in the human retina are highly heterogeneous with their abundance varies by several orders of magnitude. To decipher the complexity of gene expression and regulation of the human retinal cell types, we generated a multi-omics single-cell atlas of the adult human retina, including over 250K nuclei for single-nuclei RNA-seq and 150K nuclei for single-nuclei ATAC-seq. Over 60 cell subtypes have been identified based on their transcriptomic profiles, reaching a sensitivity of 0.01%. Integrative analysis of this single-cell multi-omics dataset identified gene regulatory elements across the genome for each cell subtype. In addition, when combined with other data modalities, such as eQTL, potential causal variants can be identified through fine mapping. Taken together, this new dataset represents the most comprehensive single-cell multi-omics profiling for the human retina that enables in-depth molecular characterization of most cell subtypes.

2023-03-14 | GSE226108 | GEO

High spatial resolution multi-omics atlas sequencing of mouse embryos

Project description:Microfluidic deterministic barcoding of mRNAs and proteins in tissue slides followed by high throughput sequencing enables the construction of high-spatial-resolution multi-omics atlas at the genome scale. Applying it to mouse embryo tissues revealed major tissue (sub)types in early-stage organogenesis, brain micro-vasculatures, and the fine structure of an optical vesicle at the single-cell-layer resolution.

2020-09-16 | GSE137986 | GEO

High spatial resolution multi-omics atlas sequencing of mouse embryos

Project description:High spatial resolution multi-omics atlas sequencing of mouse embryos

| PRJNA574105 | ENA

A multi-omics atlas of the human retina at single-cell resolution.

Project description:Cell classes in the human retina are highly heterogeneous with their abundance varying by several orders of magnitude. Here, we generated and integrated a multi-omics single-cell atlas of the adult human retina, including more than 250,000 nuclei for single-nuclei RNA-seq and 137,000 nuclei for single-nuclei ATAC-seq. Cross-species comparison of the retina atlas among human, monkey, mice, and chicken revealed relatively conserved and non-conserved types. Interestingly, the overall cell heterogeneity in primate retina decreases compared with that of rodent and chicken retina. Through integrative analysis, we identified 35,000 distal cis-element-gene pairs, constructed transcription factor (TF)-target regulons for more than 200 TFs, and partitioned the TFs into distinct co-active modules. We also revealed the heterogeneity of the cis-element-gene relationships in different cell types, even from the same class. Taken together, we present a comprehensive single-cell multi-omics atlas of the human retina as a resource that enables systematic molecular characterization at individual cell-type resolution.

| S-EPMC10300490 | biostudies-literature

Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Microfluidics]

Project description:Here we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the single-cell transcriptomic atlas of the human retina. Using a multi-resolution network-based analysis, we identify all major retinal cell types, and their corresponding gene expression signatures.

2019-09-21 | GSE137537 | GEO

Single-cell Transcriptomic Atlas of the Human Retina Identifies Cell Types Associated with Age-Related Macular Degeneration [Seq-Well]

2019-09-23 | GSE137846 | GEO

Multi-omics atlas of combinatorial abiotic stress responses in wheat

Project description:Multi-omics atlas of combinatorial abiotic stress responses in wheat

| PRJNA758708 | ENA

Single nucleus multi-omics regulatory atlas of the murine pituitary

Project description:Single nucleus multi-omics regulatory atlas of the murine pituitary

| PRJNA637893 | ENA

A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche - Visium

Project description:Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).

2022-01-06 | E-MTAB-11640 | biostudies-arrayexpress

Multi-omics profiling of mouse gastrulation at single cell resolution

Project description:Multi-omics profiling of mouse gastrulation at single cell resolution

| PRJNA498124 | ENA