Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities

PROVIDER: PRJNA508200 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8279891.fastq.gz	Fastqsanger.gz
	SRR8281054.fastq.gz	Fastqsanger.gz
	SRR8292120.fastq.gz	Fastqsanger.gz
	SRR8293150.fastq.gz	Fastqsanger.gz
	SRR8293160.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 73

Similar Datasets

Homo sapiens

Project description:Orthologous CRISPR-Cas9 for Combinatorial Genetic Screens

| PRJNA385828 | ENA

Homo sapiens

Project description:CRISPR genetic screens

| PRJNA322191 | ENA

Homo sapiens

Project description:Optimized sgRNA design to maximize activity and minimize off-target effects for genetic screens with CRISPR-Cas9

| PRJNA294629 | ENA

Homo sapiens

Project description:Optimized sgRNA design to maximize activity and minimize off-target effects for genetic screens with CRISPR-Cas9 raw sequence reads

| PRJNA294609 | ENA

Optimized CRISPR guide RNA library cloning reduces skew and enables more compact genetic screens

Project description:The development of CRISPR genetic screening tools has improved functional genomics, as these tools enable precise genomic editing, provide broad access to genomic regions beyond protein-coding genes, and have fewer off-target effects than other functional genomics modalities, allowing for novel applications with smaller library sizes compared to prior technologies. Pooled functional genomics screens require high cellular coverage per perturbation to accurately quantify phenotypes and average out phenotype-independent variability across the population. While more compact libraries have decreased the number of cells needed for a given screen, the cell coverage required for large-scale CRISPR screens still poses technical hurdles to screen in more challenging systems, such as iPSC-derived and primary cells. A major factor that influences cell coverage is screening library uniformity, as larger variation in individual guide RNA abundance requires higher cell coverage to reliably measure low-abundance guides. In this work, we have systematically optimized guide RNA cloning procedures to decrease bias. We implement these protocols to demonstrate that CRISPRi screens using 10-fold fewer cells than the current standard provides equivalent statistically significant hit-calling results to screens run at higher coverage, opening the possibility of conducting genome-wide and other large-scale CRISPR screens in technically challenging models.

2023-01-10 | GSE222531 | GEO

Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform

Project description:Systematic mapping of genetic interactions and interrogation of the functions of sizeable genomic segments in mammalian cells represent important goals of biomedical research. To advance these goals, we present a CRISPR-based screening system for combinatorial genetic manipulation that employs co-expression of Cas9 and Cas12a nucleases and machine learning-optimized libraries of hybrid Cas9-Cas12a guide RNAs. This system, named CHyMErA (Cas Hybrid for Multiplexed Editing and Screening Applications), outperforms genetic screens using Cas9 or Cas12a editing alone. Application of CHyMErA to the ablation of mammalian paralog gene pairs reveals extensive genetic interactions and uncovers phenotypes normally masked by functional redundancy. Application of CHyMErA in a chemo-genetic interaction screen identifies genes that impact cell growth in response to mTOR pathway inhibition. Moreover, by systematically targeting thousands of alternative splicing events, CHyMErA identifies exons underlying human cell line fitness. CHyMErA thus represents an effective screening approach for genetic interaction mapping and the functional analysis of sizeable genomic regions, such as alternative exons.

2020-02-29 | GSE144078 | GEO

Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform

2020-01-28 | GSE144281 | GEO

Homo sapiens

Project description:CRISPR/Cas9 Screens Reveal Epstein-Barr virus Synthetic Lethal Targets

| PRJNA361554 | ENA

Homo sapiens

Project description:An enhanced CRISPR repressor for targeted genetic screens

| PRJNA451252 | ENA

Investigation of genetic dependencies in atypical teratoid rhabdoid tumors (ATRTs) [I]

Project description:CRISPR/Cas9 knockout screens were performed to identify genetic dependencies of ATRT cell lines.

2024-10-01 | GSE230742 | GEO