Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: ParSE-seq: A High-throughput Calibrated Multiplexed Splicing Assay

PROVIDER: PRJNA1106089 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28840559_1.fastq.gz	Fastqsanger.gz
	SRR28840559_2.fastq.gz	Fastqsanger.gz
	SRR28840560_1.fastq.gz	Fastqsanger.gz
	SRR28840560_2.fastq.gz	Fastqsanger.gz
	SRR28840561_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

High-throughput high-multiplexed screening for splicing factors

Project description:High-throughput high-multiplexed screening for splicing factors

| PRJNA854891 | ENA

Comparative analysis of single-cell RNA sequencing methods with and without sample multiplexing

Project description:Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating biological heterogeneity at the single-cell level in human systems and model organisms. Recent advances in scRNA-seq have enabled the pooling of cells from multiple samples into single libraries, thereby increasing sample throughput while reducing technical batch effects, library preparation time, and the overall cost. However, a comparative analysis of scRNA-seq methods with and without sample multiplexing is lacking. In this study, we benchmarked methods from two representative platforms: Parse Biosciences (Parse; with sample multiplexing) and 10X Genomics (10x; without sample multiplexing). By using peripheral blood mononuclear cells (PBMCs) obtained from two healthy individuals, we demonstrate that demultiplexed scRNA-seq data obtained from Parse showed similar cell type frequencies compared to 10X data where samples are not multiplexed. Despite a relatively lower library and cell capture efficiencies, Parse can detect rare cell types (e.g., plasmablasts and dendritic cells) which is likely due to its relatively higher sensitivity in gene detection. Moreover, comparative analysis of transcript quantification between the two platforms revealed platform-specific distributions of gene length and GC content. These results offer guidance for researchers in designing high-throughput scRNA-seq studies.

2024-03-24 | GSE246624 | GEO

Split-pool combinatorial barcoding sequencing of murine immune cells

Project description:Single-cell RNA sequencing experiments commonly use 10x Genomics kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. The Parse technology allows the analysis of more cells from multiple samples in a single run without using additional reagents or specialized microfluidics equipment. To assess the efficacy of both platforms, we carried out a benchmark study using biological and technical replicates of young murine thymus as a complex immune tissue. To optimally utilize the capacity of Parse high-throughput kits, we also performed sequencing of murine splenocytes from a chronic stress model and control animals.

2024-10-23 | GSE253406 | GEO

Capturing totipotency in human cells through spliceosomal repression [ATAC-seq]

Project description:Supplemented with splicing inhibitor PlaB, we realize in vitro culturing of human totipotent stem cells comparable to 2-4-cell blastomeres Assay for transposase accessible chromatin with high-throughput sequencing in hESC sand hTBLCs

2024-05-30 | GSE226229 | GEO

High-throughput Microwell-seq 2.0 reveals massively multiplexed chemical perturbation

Project description:High-throughput Microwell-seq 2.0 reveals massively multiplexed chemical perturbation

| PRJNA732361 | ENA

RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants

Project description:Single nucleotide variants (SNVs) in intronic regions have yet to be systematically investigated for their disease-causing potential. Using known pathogenic and neutral intronic SNVs (iSNVs) as training data, we develop the RegSNPs-intron algorithm based on a random forest classifier that integrates RNA splicing, protein structure and evolutionary conservation features. RegSNPs-intron shows excellent performance in evaluating the pathogenic impacts of iSNVs. Using a high-throughput functional reporter assay called ASSET-seq (ASsay for Splicing using ExonTrap and sequencing), we evaluate the impact of regSNPs-intron predictions on splicing outcome. Together, RegSNPs-intron and ASSET-seq enable effective prioritization of iSNVs for disease pathogenesis.

2019-09-30 | GSE138130 | GEO

High-throughput splicing assays identify missense and silent splice-disruptive POU1F1 variants underlying pituitary hormone deficiency

Project description:Using a high throughput splicing reporter assay, we tested 1,080 single nucleotide variants in POU1F1, a key transcription factor essential for pituitary development. Our saturation splicing effect map identifies 96 splice disruptive variants, including 14 synonymous variants, of which 8 were found in unrelated patients diagnosed with hypopituitarism.

2021-04-22 | GSE172504 | GEO

MCGILL_R4.MRNA-SEQ - samples

Project description:McGill EMC Release 4 for assay "mRNA-seq": Transcriptome profiling by high-throughput sequencing

| EGAD00001001291 | EGA

MCGILL_R4.RNA-SEQ - samples

Project description:McGill EMC Release 4 for assay "RNA-seq": Transcriptome profiling by high-throughput sequencing

| EGAD00001001290 | EGA

MCGILL_R4.BISULFITE-SEQ - samples

Project description:McGill EMC Release 4 for assay "Bisulfite-seq": Methylation profiling by high-throughput sequencing

| EGAD00001001289 | EGA