Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nanowell-based single-cell combinatorial indexed ATAC-seq

ABSTRACT: Here we present advancements in single-cell combinatorial indexed ATAC-seq (sciATAC) to measure chromatin accessibility that leverage nanowell chips to achieve atlas-scale cell throughput (>105) at low cost. Our optimized techniques also achieve a high fraction of reads that fall within called peaks (>80%) and low cell doublet rates. We also demonstrate an alternative workflow that achieves high cell coverage while retaining exceptional enrichment for open chromatin regions, enabling the assessment of >70,000 unique accessible loci per cell.

ORGANISM(S): Mus musculus

PROVIDER: GSE218881 | GEO | 2023/02/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Nanowell-based single-cell combinatorial indexed ATAC-seq

Project description:Nanowell-based single-cell combinatorial indexed ATAC-seq

| PRJNA906077 | ENA

Scalable single-cell profiling of chromatin modifications with sciCUT&Tag

Project description:Cleavage Under Targets & Tagmentation (CUT&Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing precipitation-based methods. The efficiency of the method enabled chromatin profiling in single cells but is limited by the numbers of cells that can be profiled. Here, we describe a combinatorial barcoding strategy for CUT&Tag that harnesses a nanowell dispenser for simple, high-resolution high-throughput single-cell chromatin profiling. We describe a pipeline for single-cell indexed CUT&Tag (sciCUT&Tag) that uses SNPs to facilitate doublet-cell removal and minimize batch effects. We illustrate the optimized protocol by analysis of mouse and human cell lines, as well as human peripheral blood mononuclear cells. We have also used sciCUT&Tag for simultaneous profiling of multiple chromatin epitopes in single cells. The reduced cost, improved resolution and scalability of sciCUT&Tag make it an attractive platform to profile chromatin features in single cells.

2023-07-13 | GSE224579 | GEO

SCITO-seq: single-cell combinatorial indexed cytometry sequencing

Project description:We introduce single cell combinatorial indexed cytometry by sequencing (SCITO-seq), a single cell proteomics workflow that combines split-pool indexing and droplet-based sequencing

2021-03-31 | GSE147808 | GEO

SCITO-seq: single-cell combinatorial indexed cytometry sequencing

Project description:SCITO-seq: single-cell combinatorial indexed cytometry sequencing

| PRJNA619440 | ENA

Indexed single-cell RNA-seq of mensenchymal bone marrow cells

Project description:This data set contains single-cell RNA-seq data from CD45-Ter119-Cd41-CD71-Vibrant Dye+VCAM1+ cells, indexed for the expression of these markers as well as CD51, CD61 and CD200

2019-08-08 | GSE134098 | GEO

Indexed single-cell RNA-seq of mensenchymal bone marrow cells

Project description:Indexed single-cell RNA-seq of mensenchymal bone marrow cells

| PRJNA553770 | ENA

Optocoder: computational decoding of spatially indexed bead arrays

Project description:Optocoder: computational decoding of spatially indexed bead arrays

| PRJNA796322 | ENA

Spatial Mapping of Mouse Brain Aging through Indexed Sequencing

Project description:Here, we have developed a novel methodology called IRIS (Imaging Reconstruction using Indexed Sequencing) that enables cost-effective spatial transcriptomics profiling without relying on optical imaging. Through neighborhood interaction-based reconstruction, IRIS allows extensive analysis of large tissue sections and many replicates with adjustable mapping resolution at only a fraction of the cost of other commercial platforms. With the IRIS platform, we reconstructed a large area spatial area with two whole mouse brain coronal sections. Moreover, we also created a spatially resolved transcriptome atlas of the mouse brain and identified aging-associated changes in gene expression and spatial organization across various brain cell types. Further analysis of cell-cell interaction changes identified aging-associated foci in white matter regions enriched with inflammatory subtypes of microglia and oligodendrocytes. Overall, the IRIS methodology cost-effective and ease-of-use approach makes it broadly applicable to the studies of spatial gene expression changes in various systems.

2024-09-12 | GSE270383 | GEO

Combinatorial Indexed 10x Genomics Single-cell ATAC-seq on Human Cerebral Cortex

Project description:Combinatorial Indexed 10x Genomics Single-cell ATAC-seq on Human Cerebral Cortex

| PRJNA1082805 | ENA

Combinatorial Indexed 10x Genomics Single-cell ATAC-seq on Human Cerebral Cortex

Project description:Combinatorial Indexed 10x Genomics Single-cell ATAC-seq on Human Cerebral Cortex

| PRJNA1052879 | ENA