Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of Network-Correcting Molecules

ABSTRACT: Effect of Network-Correcting Molecules

PROVIDER: PRJNA635425 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11858800_1.fastq.gz	Fastqsanger.gz
	SRR11858800_2.fastq.gz	Fastqsanger.gz
	SRR11858801_1.fastq.gz	Fastqsanger.gz
	SRR11858801_2.fastq.gz	Fastqsanger.gz
	SRR11858802_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 245

Similar Datasets

Effect of Network-Correcting Molecules on NOTCH1 (N1)-Haploinsufficient Human Induced Pluripotent Stem Cell (iPSC)-Derived Endothelial Cells (ECs)

Project description:Effect of Network-Correcting Molecules on NOTCH1 (N1)-Haploinsufficient Human Induced Pluripotent Stem Cell (iPSC)-Derived Endothelial Cells (ECs)

| PRJNA515762 | ENA

Effect of Network-Correcting Molecules

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-01-01 | GSE151313 | GEO

Effect of Network-Correcting Molecules on NOTCH1 (N1)-Haploinsufficient Human Induced Pluripotent Stem Cell (iPSC)-Derived Endothelial Cells (ECs)

Project description:Discovery of small molecules that correct gene networks dysregulated in human disease may allow identification of therapies that treat disease at its fundamental basis by leveraging mechanism-based data. Here, we report the first broad gene network-based drug screen, which led to discovery of a drug candidate that effectively treats aortic valve disease in an animal model. We previously reported haploinsufficiency of NOTCH1 (N1) as a genetic cause of human aortic valve thickening and calcification, the third most common form of heart disease, and described the resulting gene network dysregulation in human induced pluripotent stem cell (iPSC)-derived endothelial cells (ECs). We exposed isogenic N1+/+ or N1+/– iPSC-derived ECs to each of 1595 small molecules or control and developed a machine learning approach that accurately distinguished WT or N1-haploinsufficient cells based on expression of 119 genes assayed by targeted RNA-sequencing. 9 small molecules corrected the gene network of N1+/– ECs sufficiently to be classified as WT. Among hits tested in vivo, the estrogen receptor-related alpha inverse agonist XCT790 significantly reduced aortic valve thickening, calcification, and stenosis in N1-haploinsufficient mice with shortened telomeres, which model the range of age-dependent cardiac disease observed in humans. This strategy, made feasible by human iPSC technology, next generation sequencing approaches, and machine learning, may represent a more effective path for drug discovery compared to conventional screening approaches.

2021-01-01 | GSE125299 | GEO

Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules

Project description:Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules

| PRJNA906109 | ENA

Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules [scRNA-Seq]

Project description:Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules [scRNA-Seq]

| PRJNA906114 | ENA

Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules [RNA-seq]

Project description:Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules [RNA-seq]

| PRJNA906113 | ENA

Effect of small molecules on activated astrocytes and microglia cells

Project description:This SuperSeries is composed of the following subset Series: GSE37611: Effect of small molecules on activated astrocytes GSE37612: Effect of small molecules on activated BV2 microglia cell line Refer to individual Series

2012-11-03 | E-GEOD-37613 | biostudies-arrayexpress

Effect of DNA bindng small molecules on SSRP1 genomic distribution

Project description:Effect of DNA bindng small molecules on SSRP1 genomic distribution

| PRJNA420688 | ENA

Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules [RNA-seq]

Project description:Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes sequences? that are critical for the removal of PCR amplification biases within both bulk and single-cell sequencing experiments. However, the impact that PCR and sequencing errors have on the accuracy of generating absolute counts of RNA molecules is underappreciated. We demonstrate that PCR errors and not sequencing errors are the main source of inaccuracy in sequencing data and that the use of UMIs synthesized with homotrimeric nucleoside building blocks provides a solution to pinpoint and remove errors, allowing absolute counting of sequenced molecules.

2023-06-01 | GSE218899 | GEO

Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules [scRNA-Seq]

2023-06-01 | GSE218901 | GEO