Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A single-cell genomic strategy for alternative TSSs identification [scTSS-seq]

ABSTRACT: Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. Here, we report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. Here, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNA, then dual priming oligonucleotide system to specifically enrich 5’-end tags for genomic analysis.

ORGANISM(S): Mus musculus

PROVIDER: GSE174479 | GEO | 2023/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A single-cell genomic strategy for alternative TSSs identification

Project description:A single-cell genomic strategy for alternative TSSs identification

| PRJNA730025 | ENA

A single-cell genomic strategy for alternative TSSs identification [scTSS-seq]

Project description:A single-cell genomic strategy for alternative TSSs identification [scTSS-seq]

| PRJNA730028 | ENA

Single cell RNA sequencing of skin T cells from patient with mycosis fungoides

Project description:Capture and processing of single skin T cells from patient with mycosis fungoides was performed using the Fluidigm C1 Autoprep system. Cells were loaded at a concentration of 2,000 cells/μL onto C1 integrated fluidic circuits (IFC) chips for 5-10 μm cells. All C1 capture sites were microscopically inspected to determine the sites containing only a single cell. Empty sites and those with multiple cells were excluded from further analysis. ERCC (External RNA Controls Consortium) spike-in RNAs were added and served as a control. SMARTer Ultra Low RNA Kit (Clontech) was used for reverse transcription and cDNA preamplification. The cDNA products from each cell were then used to prepare Illumina sequencing libraries and then sequenced on Illumina HiSeq2500 using single-end 100-base reads. Gene expression was quantified using Kallisto and then normalized to TPM values

2021-08-18 | GSE179841 | GEO

Single-cell RNA-seq investigation of skin and blood T cells from patients with cutaneous T-cell lymphoma

Project description:Capture and processing of single skin and blood T cells was performed using the Fluidigm C1 Autoprep system. Cells were loaded at a concentration of 2,000 cells/µL onto C1 integrated fluidic circuit chips for 5–10-µm cells. All C1 capture sites were microscopically inspected to identify the sites that contained only a single cell. Empty sites and those with multiple cells were excluded from further analysis. External RNA Controls Consortium spike-in RNAs served as a control. The SMARTer® Ultra® Low RNA Kit (Clontech) was used for reverse transcription and cDNA pre-amplification. The single-cell cDNA products from each cell were then used to prepare Illumina sequencing libraries and sequenced as paired-end 150-base reads on the Illumina HiSeq 4000 platform. Quality control was performed using FastQC v. 0.11.7 (Babraham Bioinformatics), and the adaptors and low-quality bases with a Phred quality score <20 were trimmed from the ends of the reads using Trim Galore v. 0.4.4 (Babraham Bioinformatics)

2023-12-28 | GSE224449 | GEO

Single cell RNA-sequencing of Spike-ins and mESC using SMARTer on C1 System

Project description:In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. We perform scRNA-seq on a homogenous population of mouse embryonic stem cells along with two kinds of control spike-in molecules to assess sensitivity and accuracy of these specific methods. In this dataset, we perform SMARTer method on Fluidigm C1 system and generate single-cell libraries using Nextera XT kit

2017-03-28 | E-MTAB-5483 | biostudies-arrayexpress

scRNA-seq of vertebrobasilar aneurysm in polyarteritis nodosa patient

Project description:Endovascular biopsy and fluorescence activated cell sorting was used to enrich for viable endothelial cells (ECs) from a vertebrobasilar aneurysm and the femoral artery. scRNAseq was then performed on 24 aneurysmal endothelial cells and 23 patient-matched non-aneurysmal femoral artery endothelial cells. cDNA libraries were prepared using the Smart-seq2 protocol on a Fluidigm C1 system (Fluidigm, South San Francisco, California) and sequenced on a HiSeq2500 machine (Illumina, San Diego, California).

2021-07-01 | E-MTAB-10681 | biostudies-arrayexpress

Single cell RNA-seq of 186 basal and luminal epithelial cells from the mammary gland of adult mice

Project description:Mammary glands of 8 adult (10 week-old) female mice were collected. Freshly sorted basal and luminal epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100bp paired-end reads.

2017-11-20 | GSE95432 | GEO

Single cell RNA-seq of 444 epithelial cells from the mammary glands of pubescent and adult mice

Project description:Mammary glands were collected from 8 pubescent (4.7-4.9 week-old) female mice and 8 adult (10 week old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads.

2017-11-20 | GSE95445 | GEO

Single cell RNA-seq of 346 epithelial cells from the mammary glands of pre-pubescent, pubescent and adult mice

Project description:Mammary glands were collected from pre-pubescent (2 weeks old), pubescent (4.7- 4.9 weeks old) and adult (10 week-old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under a microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100 bp paired-end reads.

2017-11-20 | GSE95434 | GEO

Single cell RNA-seq of 312 basal epithelial cells from the mammary glands of pregnant and adult mice

Project description:Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 adult (10 week old) female mice. Basal epithelial cells were FACS sorted. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads.

2017-11-20 | GSE95448 | 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