Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GO-CRISPR: a highly controlled workflow to improve discovery of gene essentiality

ABSTRACT: GO-CRISPR: a highly controlled workflow to improve discovery of gene essentiality

PROVIDER: PRJNA631657 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11767771.fastq.gz	Fastqsanger.gz
	SRR11767772.fastq.gz	Fastqsanger.gz
	SRR11767773.fastq.gz	Fastqsanger.gz
	SRR11767774.fastq.gz	Fastqsanger.gz
	SRR11767775.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 13

Similar Datasets

GO-CRISPR: a highly controlled workflow to improve discovery of gene essentiality

Project description:Genome-wide CRISPR screens aid researchers in discovering genes that function across a broad range of cellular mechanisms. Loss-of-function screens are particularly useful for identifying essential genes through loss of cell fitness measurements. However, loss-of-function screens are more challenging compared to gain-of-function screens due to the limited dynamic range of decreased sgRNA sequence detection. Here we describe Guide-Only control CRISPR (GO-CRISPR), an improved loss-of-function screening workflow, and its companion software package, Toolset for the Ranked Analysis of GO-CRISPR Screens (TRACS; https://github.com/developerpiru/TRACS). We demonstrate a typical GO-CRISPR workflow in a non-proliferative 3D spheroid model of dormant high grade serous ovarian cancer. We compare the results from our GO-CRISPR screen and demonstrate the discovery of novel pathways that were not possible using the currently established CRISPR screening method.

2023-04-01 | GSE150246 | GEO

GO-CRISPR: A highly controlled workflow to discover gene essentiality in loss-of-function screens.

Project description:Genome-wide CRISPR screens are an effective discovery tool for genes that underlie diverse cellular mechanisms that can be scored through cell fitness. Loss-of-function screens are particularly challenging compared to gain-of-function because of the limited dynamic range of decreased sgRNA sequence detection. Here we describe Guide-Only control CRISPR (GO-CRISPR), an improved loss-of-function screening workflow, and its companion software package, Toolset for the Ranked Analysis of GO-CRISPR Screens (TRACS). We demonstrate a typical GO-CRISPR workflow in a non-proliferative 3D spheroid model of dormant high grade serous ovarian cancer and demonstrate superior performance to standard screening methods. The unique integration of the pooled sgRNA library quality and guide-only controls allows TRACS to identify novel molecular pathways that were previously unidentified in tumor dormancy and undetectable to analysis packages that lack the guide only controls. Together, GO-CRISPR and TRACS can robustly improve the discovery of essential genes in challenging biological scenarios such as growth arrested cells.

| S-EPMC11654918 | biostudies-literature

Project description:Oryza sativa Japonica Group GO, Glutamate carboxypeptidase, Hormone homeostasis, Regulation of developmental processe, is differentially expressed in 20 experiment(s);

| Os03g0790600 | ExpressionAtlas

Project description:Oryza sativa Japonica Group GO, Glutamate carboxypeptidase, Hormone homeostasis, Regulation of developmental processe, is expressed in 7 baseline experiment(s);

| Os03g0790600 | ExpressionAtlas

Go Type 2 Diabetes

Project description:Go Type 2 Diabetes

| PRJNA268369 | ENA

Systematic evaluation of conditional gene essentiality changes across 4 yeast strains

Project description:The extent by which different genetic backgrounds affect conditional gene essentiality is understudied. Here, 4 whole-genome knockout libraries were screened to systematically record changes in conditional gene essentiality. Gene expression changes between the reference strain and the other three were measured to gain more knowledge on the molecular determinants of these changes.

2018-11-30 | GSE123118 | GEO

Reframing gene essentiality in terms of adaptive flexibility

Project description:Essentiality assays are commonly practiced as important tools for the discovery of gene functions. Growth/no growth screens of single gene knockout strain collections are often utilized to test the predictive power of genome-scale models. False positive predictions occur when computational analysis predicts a gene to be non-essential, however experimental screens deem the gene to be essential. One explanation for this inconsistency is that the model contains the wrong information, possibly an incorrectly annotated alternative pathway or isozyme reaction. Inconsistencies could also be attributed to experimental limitations, such as growth tests with arbitrary time cut-offs. The focus of this study was to resolve such inconsistencies to better understand isozyme activities and gene essentiality. Gene-deletion strains associated with false positive predictions of gene essentiality on defined minimal medium for Escherichia coli were targeted for extended growth tests followed by population sequencing.

2018-07-19 | GSE117303 | GEO

Listeria monocytogenes gene essentiality

Project description:Listeria monocytogenes gene essentiality under laboratory conditions and during macrophage infection

| PRJEB51140 | ENA

Streptomyces sp. Go-475

Project description:Streptomyces sp. Go-475 Genome sequencing and assembly

| PRJNA430025 | ENA

Thalassospira sp. GO-4

Project description:Thalassospira sp. GO-4 Genome sequencing and assembly

| PRJNA841389 | ENA