Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CRISPRi with barcoded expression reporters dissects regulatory networks in human cells

ABSTRACT: CRISPRi with barcoded expression reporters dissects regulatory networks in human cells

PROVIDER: PRJNA1154595 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR30485921.fastq.gz	Fastqsanger.gz
	SRR30485922.fastq.gz	Fastqsanger.gz
	SRR30485923.fastq.gz	Fastqsanger.gz
	SRR30485924.fastq.gz	Fastqsanger.gz
	SRR30485925.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 43

Similar Datasets

CRISPRi with barcoded expression reporters dissects regulatory networks in human cells

Project description:Genome-wide CRISPR screens have emerged as powerful tools for uncovering the genetic underpinnings of diverse biological processes. Incisive screens often depend on directly measuring molecular phenotypes, such as regulated gene expression changes, provoked by CRISPR-mediated genetic perturbations. Here, we provide quantitative measurements of transcriptional responses in human cells across genome-scale perturbation libraries by coupling CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). To enable CiBER-seq in mammalian cells, we optimize the integration of highly complex, barcoded sgRNA libraries into a defined genomic context. CiBER-seq profiling of a nuclear factor kappa B (NF-κB) reporter delineates the canonical signaling cascade linking the transmembrane TNF-alpha receptor to inflammatory gene activation and highlights cell-type-specific factors in this response. Importantly, CiBER-seq relies solely on bulk RNA sequencing to capture the regulatory circuit driving this rapid transcriptional response. Our work demonstrates the accuracy and potential of CiBER-seq for dissecting genetic networks in mammalian cells with superior time resolution.

2024-09-09 | GSE276055 | GEO

CRISPRi with barcoded expression reporters dissects regulatory networks in human cells.

Project description:Genome-wide CRISPR screens have emerged as powerful tools for uncovering the genetic underpinnings of diverse biological processes. Incisive screens often depend on directly measuring molecular phenotypes, such as regulated gene expression changes, provoked by CRISPR-mediated genetic perturbations. Here, we provide quantitative measurements of transcriptional responses in human cells across genome-scale perturbation libraries by coupling CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). To enable CiBER-seq in mammalian cells, we optimize the integration of highly complex, barcoded sgRNA libraries into a defined genomic context. CiBER-seq profiling of a nuclear factor kappa B (NF-κB) reporter delineates the canonical signaling cascade linking the transmembrane TNF-alpha receptor to inflammatory gene activation and highlights cell-type-specific factors in this response. Importantly, CiBER-seq relies solely on bulk RNA sequencing to capture the regulatory circuit driving this rapid transcriptional response. Our work demonstrates the accuracy of CiBER-seq and its potential for dissecting genetic networks in mammalian cells with superior time resolution.

| S-EPMC11398470 | biostudies-literature

CiBER-seq dissects genetic networks by quantitative CRISPRi profiling of expression phenotypes.

Project description:To realize the promise of CRISPR-Cas9-based genetics, approaches are needed to quantify a specific, molecular phenotype across genome-wide libraries of genetic perturbations. We addressed this challenge by profiling transcriptional, translational, and posttranslational reporters using CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). Our barcoding approach allowed us to connect an entire library of guides to their individual phenotypic consequences using pooled sequencing. CiBER-seq profiling fully recapitulated the integrated stress response (ISR) pathway in yeast. Genetic perturbations causing uncharged transfer RNA (tRNA) accumulation activated ISR reporter transcription. Notably, tRNA insufficiency also activated the reporter, independent of the uncharged tRNA sensor. By uncovering alternate triggers for ISR activation, we illustrate how precise, comprehensive CiBER-seq profiling provides a powerful and broadly applicable tool for dissecting genetic networks.

| S-EPMC7819735 | biostudies-literature

Ascertaining cells' synaptic connections and RNA expression simultaneously with barcoded rabies virus libraries

Project description:We describe "SBARRO" a system in which synaptic networks of cells are reconstructed from scRNA-seq data using clonal infectivity paths of barcoded rabies virus RNAs

2022-10-06 | GSE214386 | GEO

RNA-seq of CSMD1 enhancer CRISPRi in LUHMES cells and differentiated neurons

Project description:we performed lentiviral CRISPR interference (CRISPRi) by recruiting dCas9 fused with the KRAB domain to the CSMD1 enhancer (fam3) in the neuronal precursor cell line – Lund human mesencephalic (LUHMES). Given that the expression of CSMD1 was not detectable in LUHMES cells we differentiated these cells into neurons. Differentiated neurons with CRISPRi of CSMD1 enhancer showed significantly higher expression of CSMD1 than control.

2022-06-30 | E-MTAB-8027 | biostudies-arrayexpress

Saccharomyces cerevisiae S288C

Project description:CiBER-seq dissects genetic networks by quantitative CRISPRi profiling of expression phenotypes

| PRJNA578818 | ENA

iPSC RNA-seq upon CRISPRn or CRISPRi manipulation

Project description:Assess the on- and off-target effects of dox-inducible CRISPR/Cas9 and CRISPRi constructs in a human iPS cell line. Transcript quantification of 3 cell lines, each plus or minus doxycycline and with or without specific single guide RNAs (sgRNAs), with 2 biological replicates each.

2016-01-19 | E-GEOD-76980 | biostudies-arrayexpress

Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.

Project description:Cis-regulatory DNA sequences causally mediate patterns of gene expression, but efficient experimental analysis of these control systems has remained challenging. Here we develop a new version of "barcoded" DNA-tag reporters, "Nanotags" that permit simultaneous quantitative analysis of up to 130 distinct cis-regulatory modules (CRMs). The activities of these reporters are measured in single experiments by the NanoString RNA counting method and other quantitative procedures. We demonstrate the efficiency of the Nanotag method by simultaneously measuring hourly temporal activities of 126 CRMs from 46 genes in the developing sea urchin embryo, otherwise a virtually impossible task. Nanotags are also used in gene perturbation experiments to reveal cis-regulatory responses of many CRMs at once. Nanotag methodology can be applied to many research areas, ranging from gene regulatory networks to functional and evolutionary genomics.

| S-EPMC3339872 | biostudies-literature

Precise measurement of molecular phenotypes with barcode-based CRISPRi screens

Project description:Uncovering the genetic basis of molecular processes is essential for understanding a broad range of biological phenomena. CRIPSR-Cas9 approaches enable this discovery through programable and systematic profiling of regulatory genes underlying diverse cellular behaviors. A key challenge for dissecting genetic networks is expanding CRISPR-based screens to interrogate specific phenotypes with high precision. Here, we use a quantitative, sequencing-based CRISPRi platform to enhance the scope and sensitivity of genome-wide screens. We first systematically explore how technical variations distort guide effects and correct for these factors by using RNA reporters and normalizers expressed from closely matched promoters. We then combine this platform with a recombinase-based integration system to interrogate protein and RNA-level phenotypes. We find our approach accurately captures known regulators of protein or RNA quality control with high accuracy and minimal background. These barcode-based CRISPR systems provide a powerful and generalizable platform for dissecting critical cellular regulatory pathways.

2024-06-12 | GSE268777 | GEO

EMS02 barcoded yeast collection

Project description:EMS02 barcoded yeast collection

| PRJEB90659 | ENA