Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A simple and robust plate-based single-cell ATAC-seq on various tissues and cell lines

ABSTRACT: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is widely used to identify regulatory regions throughout the genome. However, only a few studies have been done at the single cell level (scATAC-seq) due to technical difficulties. Here we developed a simple and robust plate-based scATAC-seq method, combining upfront bulk tagmentation with single-nuclei sorting, to investigate open chromatin regions. We applied this method on mouse splenocytes and unbiasedly revealed key regulatory regions and transcription factors that define each cell (sub)type.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): mixed sample

SUBMITTER: Xi Chen

PROVIDER: E-MTAB-6714 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scATAC-seq of mouse Plasmodium-specific CD4+ T cells

Project description:Plasmodium-specific CD4+ T cells from mice infected with Plasmodium chabaudi chabaudi AS parasites were recovered at Days 0, 4, 7, and 32 to undergo processing and to generate scATAC-seq dataset. At Day 7, CXCR5+ and CXCR6+ cells were recovered separately. At Day 32, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). scATAC-seq dataset was analysed to investigate epigenomic landscapes of CD4+ T cells from effector to memory states.

2020-10-14 | E-MTAB-9402 | biostudies-arrayexpress

Single-cell chromatin accessibility atlas of human retinal organoid development

Project description:In order to provide multi-omic resolution to human retinal organoid developmental dynamics, we performed scRNA-seq and scATAC-seq from the same cell suspension across a time course (6-46 weeks) of human retinal organoid development. This data set covers all the retinal organoid scATAC-seq data generated from IMR90 and 409B2-iCas9 cell lines.

2023-03-12 | E-MTAB-12714 | biostudies-arrayexpress

The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation (ChIP-seq)

Project description:The IRE1a-XBP1 pathway, a conserved adaptive response to the unfolded protein response, is indispensable for development of the secretory cells. It maintains endoplasmic reticulum homeostasis by enhancing protein folding and the secretory capacity of the cells. Here, we used a modified ChIP-seq protocol (ChIPmentation) to investigate the genome-wide binding events of the transcription factor XBP1 in differentiated mouse Th2 cells.

2018-10-06 | E-MTAB-6327 | biostudies-arrayexpress

Single cell profiling of a Caki-1:HeLa cell mixture by scATAC-seq and scGET-seq

Project description:A mixture of Caki-1 and HeLa cells in known proportions (80:20) is profiled using 10x Chromium scATAC-seq or scGET-seq protocols.

2021-08-17 | E-MTAB-9650 | biostudies-arrayexpress

Single-cell transcriptional analysis reveals innate lymphoid cell (ILC)-like cells in zebrafish

Project description:Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tg(cd4-1:mCherry), Tg(lck:EGFP), Tg(mhc2dab:GFP, cd45:dsRed), AB.

2018-11-16 | E-MTAB-7117 | biostudies-arrayexpress

T helper cell type 2 ATAC-seq time-course

Project description:CD4+ T cells were extracted from mouse and human. They were activated in vitro with CD3/28 and cultured with Il4. ATAC-seq was then performed at different time points

2017-12-14 | E-MTAB-6292 | biostudies-arrayexpress

Multi-modal single-cell sequencing of differentiating mESCs using Smart-seq3 and scATAC-seq

Project description:We report dynamics of X-chromosome upregulation (XCU) along X-chromosome inactivation (XCI) in mESCs as they differentiate into EpiSCs. F1 hybrid C57BL6/J × CAST/EiJ male and female mESCs were grown in serum/LIF conditions were differentiated using Fgf2 and Activin A for 1, 2, 4 and 7 days to induce random XCI in female cells. Multi-modal single-cell sequencing was performed using scATAC on nuclei and Smart-seq3 to assay chromatin accessibility and poly-A+ RNA expression, respectively. Allelic resolution is achieved using strain-specific SNPs in the data. We reveal dynamic balancing of X alleles as cells undergo XCI to compensate dosage imbalances between sexes as well as between X and autosomes. Furthermore, we reveal that female naïve mESCs with two active X chromosomes lack XCU on both alleles which has major implications for reprogramming studies. Finally, we estimate allelic transcriptional burst kinetics from the data and find that progressively increased burst frequencies underlies the XCU process.

2022-02-14 | E-MTAB-10714 | biostudies-arrayexpress

T helper cell type 2 ChIP-seq

Project description:CD4+ T cells were extracted from mouse and human. They were activated in vitro with CD3/28 and cultured with Il4. ChIPmentation was then performed

2017-12-06 | E-MTAB-6276 | biostudies-arrayexpress

Single Cell Multi-Omics Profiling Using ISSAAC-seq

Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.

2022-06-15 | E-MTAB-11264 | biostudies-arrayexpress

Single-cell transcriptome atlas of human retinal organoid development

Project description:In order to provide multi-omic resolution to human retinal organoid developmental dynamics, we performed scRNA-seq and scATAC-seq from the same cell suspension across a time course (6-46 weeks) of human retinal organoid development. This data set covers all the retinal organoid scRNA-seq data generated from IMR90 and409B2-iCas9 cell lines.

2023-03-12 | E-MTAB-12715 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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