GEO DataSets

(Submitter supplied) Single-cell measurements of cellular characteristics have been instrumental in understanding the heterogeneous pathways that drive differentiation, cellular responses to signals, and human disease. Recent advances have allowed paired capture of protein abundance and transcriptomic state, but a lack of epigenetic information in these assays has left a missing link to gene regulation. Using the heterogeneous mixture of cells in human peripheral blood as a test case, we developed a novel scATAC-seq workflow that increases signal-to-noise and allows paired measurement of cell surface markers and chromatin accessibility: Integrated Cellular Indexing of Chromatin Landscape and Epitopes (ICICLE-seq). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL18573

34 Samples

Download data: CSV, H5, TSV

(Submitter supplied) Recent technological advances have enabled massively parallel single-cell Assay for Transposase Accessible Chromatin by sequencing (scATAC-seq) to simultaneously profile the epigenomic landscape in thousands of individual cells. scATAC-seq methods sample genomic DNA accessible to transposases, but have not previously been combined with measurement of protein levels. Here, we present ATAC with Select Antigen Profiling by sequencing, ASAP-seq, a tool to simultaneously profile accessible chromatin and protein levels in thousands of single cells, pairing sparse scATAC data with robust detection of hundreds of cell surface and intracellular protein markers, and optionally, enriched mtDNA coverage for lineage tracing (mtscATAC-seq) with minimal impact on ATAC-seq data quality. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL24676

6 Samples

Download data: CSV, TSV, TXT

(Submitter supplied) Recent technological advances have enabled massively parallel single-cell Assay for Transposase Accessible Chromatin by sequencing (scATAC-seq) to simultaneously profile the epigenomic landscape in thousands of individual cells. scATAC-seq methods sample genomic DNA accessible to transposases, but have not previously been combined with measurement of protein levels. Here, we present ATAC with Select Antigen Profiling by sequencing, ASAP-seq, a tool to simultaneously profile accessible chromatin and protein levels in thousands of single cells, pairing sparse scATAC data with robust detection of hundreds of cell surface and intracellular protein markers, and optionally, enriched mtDNA coverage for lineage tracing (mtscATAC-seq) with minimal impact on ATAC-seq data quality. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

12 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL24625 GPL21697 GPL24676

52 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) We developed HyDrop, a new droplet microfluidic single-cell sequencing protocol for single-cell ATAC-seq and single-cell RNA-seq. We applied HyDrop-ATAC to flash-frozen mouse cortex and generated 7996 single-cell chromatin accessibility profiles. We applied HyDrop-RNA to flash-frozen mouse cortex and generated 9508 single-cell transcriptomes. We also applied HyDrop-RNA to a small population of FAC-sorted neurons from the Drosophila brain to demonstrate the protocol's applicability to low-input samples. more...

Organism:

Homo sapiens; Mus musculus; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms

20 Samples

Download data: BW, TAR, TSV

(Submitter supplied) While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

5 Samples

Download data: CSV

(Submitter supplied) While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21697 GPL24625

4 Samples

Download data: CSV, TSV, XLSX

(Submitter supplied) While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24625

6 Samples

Download data: CSV, TSV, XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21626 GPL24625 GPL21697

82 Samples

Download data: CSV, TBI, TSV

(Submitter supplied) While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

16 Samples

Download data: BED, CSV, TBI, TSV, XLSX

(Submitter supplied) While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24625

5 Samples

Download data: CSV, TSV, XLSX

(Submitter supplied) While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

28 Samples

Download data: BED, CSV, TBI, TSV, XLSX

(Submitter supplied) While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

6 Samples

Download data: BED, CSV, TBI, TSV, XLSX

(Submitter supplied) While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

12 Samples

Download data: BED, CSV, TBI, TSV, XLSX

(Submitter supplied) The naïve T cell compartment undergoes multiple changes across age that associate with altered susceptibility to infection and autoimmunity. In addition to the acquisition of naïve-like memory T cell subsets, recent murine studies describe substantial molecular reprogramming of the naïve compartment in adults compared with adolescents. However, these alterations are not well delineated in human aging. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL24676

109 Samples

Download data: CSV, H5, TSV

(Submitter supplied) Tumors show substantial amounts of cellular heterogeneity by forming complex ecosystems of malignant and non-malignant cells. Herein, we present a comprehensive multi-omic cell atlas of matched single-cell transcriptome and single-cell chromatin accessibility profiles spanning over 150,000 cells from 11 human gynecologic tumors. By jointly analyzing these transcriptomic and chromatin accessibility profiles at single-cell resolution, we identify 115,734 total peak-to-gene links representing putative regulatory interactions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

22 Samples

Download data: MTX, TSV

(Submitter supplied) BABEL enables cross-modality translation between multi-omic profiles at single-cell resolution

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: H5, TSV

(Submitter supplied) Normal human hematopoiesis involves cellular differentiation of multipotent cells into progressively more lineage-restricted states. While epigenomic landscapes of this process have been explored in immunophenotypically-defined populations, the single-cell regulatory variation that defines hematopoietic differentiation has been hidden by ensemble averaging. We generated single-cell chromatin accessibility landscapes across 8 populations of immunophenotypically-defined human hematopoietic cell types. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL18573

2805 Samples

Download data

(Submitter supplied) Normal human hematopoiesis involves cellular differentiation of multipotent cells into progressively more lineage-restricted states. While epigenomic landscapes of this process have been explored in immunophenotypically-defined populations, the single-cell regulatory variation that defines hematopoietic differentiation has been hidden by ensemble averaging. We generated single-cell chromatin accessibility landscapes across 8 populations of immunophenotypically-defined human hematopoietic cell types. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

13 Samples

Download data: TXT