Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Droplet-based single-cell RNA-sequencing facilitates transcription analysis of small intestine epithelial cells from SubAA273IEC and littermate control

ABSTRACT: Droplet-based single-cell RNA-sequencing facilitates transcription analysis of small intestine epithelial cells from SubAA273IEC and littermate control

PROVIDER: PRJNA841345 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19349289.fastq.gz	Fastqsanger.gz
	SRR19349290.fastq.gz	Fastqsanger.gz
	SRR19349291.fastq.gz	Fastqsanger.gz
	SRR19349292.fastq.gz	Fastqsanger.gz
	SRR19349293.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Droplet-based single-cell RNA-sequencing facilitates transcription analysis of small intestine epithelial cells from SubAA273IEC and littermate control

Project description:We performed theDroplet-based single-cell RNA-sequencing on small intestine epithelial cells from SubAA273IEC and littermate control and found the effect of ER stress in epithelia cells on epithelial cells.

2023-03-13 | GSE203538 | GEO

Droplet-based single-cell RNA-sequencing facilitates trancritption analysis of small intestine CD4 cells from Germline free Xbp1ΔIEC and Xbp1fl/fl

Project description:Droplet-based single-cell RNA-sequencing facilitates trancritption analysis of small intestine CD4 cells from Germline free Xbp1ΔIEC and Xbp1fl/fl

| PRJNA714643 | ENA

Droplet-based single-cell RNA-sequencing facilitates trancritption analysis of small intestine CD4 cells from Germline free Xbp1ΔIEC and Xbp1fl/fl

Project description:We performed theDroplet-based single-cell RNA-sequencing on small intestine CD4 cells from Germline free(GF) Xbp1ΔIEC and Xbp1fl/fl mice and found the effect of ER stress in epithelia cells on CD4 cells.

2023-03-13 | GSE168947 | GEO

3' droplet-based single cell RNA sequencing of a mouse large intestinal epitherlium

Project description:Using 3' droplet-based single-cell sequencing, we performed the transcriptional profiling of mouse large intestinal epithelial cells at the single-cell level.

2022-07-28 | GSE209649 | GEO

5' droplet-based single cell RNA sequencing of human colorectal cancer and normal organoids

Project description:Using 5' droplet-based single cell sequencing, we profiled single cells dervied from human colorectal cancer organoids carrying either APC mutation or RSPO fusion, and paired normal colon organoids for the later.

2020-03-31 | GSE142116 | GEO

Stromal inflammation is a targetable driver of hematopoietic aging [droplet-based scRNAseq]

Project description:To investigate global changes in the structure of the bone marrow niche with age, we performed droplet-based scRNAseq (10X Genomics) of unfractionated endosteal and central marrow stromal cells (Ter119-/CD45-). 8,735 cells passed QC, and hematopoietic clusters of cells were excluded based on marker gene expression, leaving 2359 cells distributed across 9 distinct clusters for final presentation.

2022-11-02 | GSE168586 | GEO

Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states

Project description:In this study, we introduce BacDrop, a bacterial droplet-based high throughput scRNA-seq technology that can be applied to large cell numbers. We applied BacDrop to study Klebsiella pneumoniae clinical isolates and elucidated their critical, genome-wide heterogeneity in the absence and presence of antibiotic perturbations.

2023-01-27 | GSE180237 | GEO

Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes

Project description:We present a high-throughput and droplet-based bisulfite sequencing library preparation platform. Our protocol allows production of BS library of 2,000-10,000 single cells within 2 days. In addition to validation using mixed cell lines, we also used the technology to profile various cell types in mouse and human brain samples.

2023-07-04 | GSE204691 | GEO

Effect of methanol fixation on single cell RNA sequencing of the murine dentate gyrus (droplet-based scRNAseq).

Project description:We evaluated the effect of methanol (MeOH) fixation on adult murine dentate gyrus (DG) single cell suspensions processed with droplet-based scRNA-seq.

2023-09-22 | GSE241452 | GEO

Cell fixation and preservation for droplet-based single cell transcriptomics

Project description:Background: Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells, in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not compromised by stress or ageing. Another challenge are rare cells that need to be collected over several days, or samples prepared at different times or locations. Results: Here, we used chemical fixation to overcome these problems. Methanol fixation allowed us to stabilize and preserve dissociated cells for weeks. By using mixtures of fixed human and mouse cells, we showed that individual transcriptomes could be confidently assigned to one of the two species. Single-cell gene expression from live and fixed samples correlated well with bulk mRNA-seq data. We then applied methanol fixation to transcriptionally profile primary single cells from dissociated complex tissues. Low RNA content cells from Drosophila embryos, as well as mouse hindbrain and cerebellum cells sorted by FACS, were successfully analysed after fixation, storage and single-cell droplet RNA-seq. We were able to identify diverse cell populations, including neuronal subtypes. As an additional resource, we provide 'dropbead', an R package for exploratory data analysis, visualization and filtering of Drop-seq data. Conclusions: We expect that the availability of a simple cell fixation method will open up many new opportunities in diverse biological contexts to analyse transcriptional dynamics at single cell resolution.

2017-05-03 | GSE89164 | 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