Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A multiplex single-cell RNA-seq pharmacotranscriptomics pipeline for drug discovery

ABSTRACT: A multiplex single-cell RNA-seq pharmacotranscriptomics pipeline for drug discovery

PROVIDER: PRJNA1148445 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR30251527.fastq.gz	Fastqsanger.gz
	SRR30251528.fastq.gz	Fastqsanger.gz
	SRR30251529.fastq.gz	Fastqsanger.gz
	SRR30251530.fastq.gz	Fastqsanger.gz
	SRR30251531.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

A multiplex single-cell RNA-seq pharmacotranscriptomics pipeline for drug discovery

Project description:We report a pipeline for high-throughput pharmacotranscriptomic profiling via 96-plexed single-cell RNA-sequencing (scRNA-Seq) using Cell Hashing. We show the potential of this approach by exploring the heterogeneous transcriptional landscape of primary high-grade serous ovarian cancer (HGSOC) cells after treatment with 45 drugs, with 13 distinct classes of mechanisms of action. A subset of PI3K/AKT/mTOR inhibitors induced the activation of receptor tyrosine kinases, such as the epithelial growth factor receptor (EGFR), and this is mediated by the upregulation of caveolin-1 (CAV1). This drug resistance feedback loop could be mitigated by the synergistic action of PI3K/AKT/mTOR- and EGFR-targeting agents for HGSOC with CAV1/EGFR expression.

2024-10-21 | GSE274905 | GEO

Next generation rare variant discovery in multiplex AD families

Project description:Next generation rare variant discovery in multiplex AD families

| PRJNA517199 | ENA

Next generation rare variant discovery in multiplex AD families

Project description:Next generation rare variant discovery in multiplex AD families

| PRJNA517200 | ENA

Massively multiplex single-cell Hi-C

Project description:Massively multiplex single-cell Hi-C

| PRJNA335638 | ENA

Massively multiplex single-molecule oligonucleosome footprinting

Project description:Massively multiplex single-molecule oligonucleosome footprinting

| PRJNA681807 | ENA

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

Project description:Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computational methods. Long-read sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) bypass the transcript reconstruction challenges of short-reads. Here we describe TALON, the ENCODE4 pipeline for analyzing PacBio cDNA and ONT direct-RNA transcriptomes. We apply TALON to three human ENCODE Tier 1 cell lines and show that while both technologies perform well at full-transcript discovery and quantification, each one displayed distinct artifacts. We further apply TALON to mouse cortical and hippocampal transcriptomes and find that a substantial proportion of neuronal genes have more reads associated with novel isoforms than with annotated ones. These data show that TALON is a technology-agnostic long-read transcriptome discovery and quantification pipeline capable of tracking both known and novel transcript models, as well as their expression levels, across datasets for both simple studies and in larger projects. These properties will enable TALON users to move beyond the limitations of short-read data to perform isoform discovery and quantification in a uniform manner on existing and future long-read platforms.

2020-03-18 | GSE147118 | GEO

Multiplex Chromatin Interactions with Single Molecule Precision

Project description:Multiplex Chromatin Interactions with Single Molecule Precision

| PRJNA430678 | ENA

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

Project description:Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computational methods. Long-read sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) bypass the transcript reconstruction challenges of short-reads. Here we describe TALON, the ENCODE4 pipeline for analyzing PacBio cDNA and ONT direct-RNA transcriptomes. We apply TALON to three human ENCODE Tier 1 cell lines and show that while both technologies perform well at full-transcript discovery and quantification, each technology has its distinct artifacts. We further apply TALON to mouse cortical and hippocampal transcriptomes and find that a substantial proportion of neuronal genes have more reads associated with novel isoforms than annotated ones. The TALON pipeline for technology-agnostic, long-read transcriptome discovery and quantification tracks both known and novel transcript models as well as expression levels across datasets for both simple studies and larger projects such as ENCODE that seek to decode transcriptional regulation in the human and mouse genomes to predict more accurate expression levels of genes and transcripts than possible with short-reads alone.

2019-06-15 | GSE132766 | GEO

Multiplex Chromatin Interactions with Single Molecule Precision

Project description:Emerging 3D genome mapping efforts suggest complex chromosomal folding structures. However, the true multiplex nature of chromatin interactions has yet to be fully explored. Here, we describe a chromatin interaction analysis by droplet-based sequencing (ChIA-Drop). In ChIA-Drop, individual chromatin complexes are partitioned into droplets that contain a gel bead of DNA-barcoded primers, such that tethered chromatin DNA fragments are uniquely indexed and amplified for sequencing and mapping to demarcate multiplex chromatin contacts. Thus, ChIA-Drop can identify complex chromatin interactions with unprecedented single-molecule precision, which is not possible using methods that analyze pairwise contacts via proximity ligation. We demonstrate that multiplex chromatin interactions predominantly contribute to topologically associated domains with high heterogeneity, and that multivalent promoter-centered interactions provide a topological model for gene transcription.

2019-02-11 | GSE109355 | GEO

Lentiviral-driven discovery of cancer drug resistance mutations

Project description:Lentiviral-driven discovery of cancer drug resistance mutations

| PRJNA750135 | ENA