Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility

ABSTRACT: We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10X Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16-/-) model. Our study of CC16-/- nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE245957 | GEO | 2023/10/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility

Project description:We develop a large-scale single-cell ATAC-seq method (txci-ATAC-seq) by combining Tn5-based pre-indexing with 10X Genomics barcoding. Leveraging this molecular hashing strategy, we demonstrate that txci-ATAC-seq enables the indexing of up to 200,000 nuclei across multiple samples in a single emulsion reaction, representing a ~22-fold increase in throughput compared to the standard workflow at the same collision rate. To improve the multiplexing capability of this new technique, we further develop a "phased" protocol variant (Phased-txci-ATAC-seq) that effectively decouples sample processing from library preparation and has the potential to profile up to 96 samples simultaneously. In this study, we profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16-/-) model. Our study of CC16-/- nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model.

2023-10-25 | GSE231708 | GEO

Bronchiolar progenitors and club cells in mouse lung

Project description:Gene expression patterns of bronchiolar progenitors and club cells in mouse lung were examined by microarray experiments. Although it has not yet been fully characterized, a subset of epithelial cells lining bronchioles are best understood as bronchiolar progenitors that self-renew over the long term and that can differentiate into more differentiated club cells and ciliated cells. The bronchiolar progenitors are distinct from club cells and characteristically express the alveolar type 2 cell marker, prosurfactant protein C, with lower levels of club cell secretory protein/Scgb1a1. There are also functional differences between them; while club cells can be depleted by naphthalene because of the abundance of cytochrome P450 enzyme Cyp2f2, bronchiolar progenitors are resistant to naphthalene-induced depletion because of defects in the enzyme.

2016-02-17 | E-MTAB-4460 | biostudies-arrayexpress

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_WT]

Project description:Chromatin accessibility and transcriptome profiling are the most critical tools in single-cell technologies. Here, we present Microwell-seq3, a high-throughput and easy-to-handle platform for high-sensitive single-nucleus chromatin accessibility or full-length gene expression profiling. The method combined pre-indexing and a dual-pass “chip-in-tube” strategy for nuclei loading and DNA amplification. Therefore, Microwell-seq3 does not require specialized equipment and is suitable for any molecular biology lab with simple consumables and thermal cycler. We applied Microwell-seq3 to profile the chromatin accessibility in more than 200,000 single nuclei and the full-length transcriptome in about 50,000 nuclei from multiple adult mouse tissues. Joint analysis of cell-type specific regulatory elements and total RNA uncovered cell type heterogeneity and differentially expressed genes in brain compared with previous polyadenylated transcripts capturing methods. Gene regulatory networks based on full-length transcriptome and chromatin accessibility provided improved cell-cell communications in neurons and glia. Finally, we applied Microwell-seq3 to comprehensively characterize malignant cells in spontaneous tumors from aging mouse.

2024-01-03 | GSE225133 | GEO

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_Tumor]

2024-01-03 | GSE225132 | GEO

RNA quantitative sequencing in TGF-beta treated PDCD5 knockdown C22 cells

Project description:The role of bronchial epithelial club (clara) cell in lung fibrosis is unclear. We found programmed cell death 5 (PDCD5) expression is elevated in lung fibrosis. To investigate the molecular mechanism by which PDCD5 mediates lung fibrosis in club cell, mouse C22 cells were analyzed by RNA-sequencing with or without Pdcd5 knockdown after TGF-beta treatment.

2021-03-17 | GSE143841 | GEO

Gene expression profiling of Scgb1a1+, CD24low cells isolated from the lungs of Scgb1a1-CreER; Rosa26-mTmG mouse.

Project description:We established a new method to find out subpopulation of lung epithelial stem cells, named scMORN, and uncovered the existence of Club cell subpopulations contributing to alveolar regeneration. We isolated entire Club cells by sorting Scgb1a1+, CD24low cells from the lungs of Scgb1a1-CreER; Rosa26-mTmG mouse. The gene expression profiling revealed that two genetically distinct types of Club cells.

2023-08-23 | GSE189917 | GEO

Club cells employ regeneration mechanisms during lung tumorigenesis

Project description:Lung adenocarcinoma (LUAD) is one of the deadliest malignancies worldwide. Dynamic lineage changes within the lung epithelium and the high plasticity of these epithelial cells confound the correct identification of the cell-of-origin of LUAD. Here, we combined lineage-tracing mouse models with an autochthonous cell type-independent LUAD model in order to discover the cellular origin of ALK-translocated LUAD. We identified Club and AT2 cells as the cells-of-origin of LUAD. Moreover, we uncovered epigenetic imprints in the tumours originating from Club or AT2 cells by whole-genome bisulfite sequencing. Single-cell transcriptomes of Club cells at different stages of tumour development identified two trajectories of Club cell evolution. On both routes, tumours lose their Club cell identity and gain an AT2-like phenotype. Together, this study highlights the role of Club cells in LUAD initiation and unveils key mechanisms conferring LUAD heterogeneity.

2022-06-30 | GSE176185 | GEO

Club cells employ regeneration mechanisms during lung tumorigenesis

2022-06-30 | GSE176184 | GEO

Transcriptomic analysis of lung cancers arising following deletion of Tp53, Rb1 and overexpression of MYC in distinct adult mouse lung eptithelial cell lineages

Project description:Profile of the transcriptomics of tumours arising in the mouse lung following deletion of Rb1, Trp53 and overexpression of MYC from neuroendocrine cells, club cells, AT2 cells or throughout the lung epithelium.

2021-10-25 | GSE161185 | GEO

A Single Cell Transcriptome Atlas of The Domestic Pig

Project description:By leveraging single-cell/nuclei RNA sequencing, we generate the first single-cell transcriptome atlas of over 200,000 pig cells from 20 tissues/organs.

2022-01-21 | GSE193975 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data