Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: CRISPRi screen and whole genome sequencing

PROVIDER: PRJEB84063 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR14126944.fastq.gz	Fastqsanger.gz
	ERR14126945.fastq.gz	Fastqsanger.gz
	ERR14126946.fastq.gz	Fastqsanger.gz
	ERR14126947.fastq.gz	Fastqsanger.gz
	ERR14126948.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

A multicenter translational biomarker phase II trial of regorafenib in patients with non-resectable pretreated colorectal cancer.

Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS). Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).

| 2533916 | ecrin-mdr-crc

Project description:CRISPRi screen & sspA

| PRJNA1109382 | ENA

BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2

Project description:We performed RNA sequencing of Calu-3 cells after treatment with the BET-domain inhibitors JQ-1 and ABBV-744 as well as BRD2 CRISPRi knockdown. We also included CRISPRi knockdown of two other validated hit genes from our screen, COMP and ACE2.

2021-01-19 | GSE165025 | GEO

Landscape of enhancer disruption and functional screen in melanoma

Project description:Here, we leveraged 297 melanoma whole-genome sequencing (WGS) samples to prioritize highly recurrent regions (HRRs). By performing a genome-scale CRISPR interference (CRISPRi) screen on HRR-associated enhancers in melanoma cells, we identified 66 significant hits which could have tumor-suppressive roles. These functional enhancers show unique mutational patterns independent of classical significantly mutated genes in melanoma. Target gene analysis for the essential enhancers revealed many known and hidden mechanisms underlying melanoma growth. Utilizing extensive functional validation experiments, we demonstrated that a super enhancer element could modulate melanoma cell proliferation by targeting MEF2A and another distal enhancer was able to sustain PTEN tumor-suppressive potential via long-range interaction.

2023-10-10 | GSE210424 | GEO

Gene expression profile at single-cell level of human Simpson-Golabi-Behdel syndrome (SGBS) cells undergoing adipogenesis following knock-down of target genes using CRISPRi

Project description:CROP-Seq combines gene silencing using CRISPR interference (CRISPRi) with single-cell RNA sequencing (scRNA-Seq) in a functional reverse genetic screen. Here, we applied the CROP-Seq approach to study the function of novel genes acting in human adipogenesis or adipocyte biology that were derived from genome-wide association studies (GWAS).

2022-11-15 | GSE217812 | GEO

Genome-wide CRISPRi screen for myriocin sensitivity

Project description:Genome-wide CRISPRi screen for myriocin sensitivity

| PRJNA644921 | ENA

Epigenetics CRISPRi screen in mouse neuronal progenitor cells (NPCs)

Project description:This dataset examined the epigenetic gene effect on mouse NPCs with Upf2 gene knockout (KO). The sgRNA sequencing results form the epigenetics CRISPRi screen sample are reported.

2024-11-06 | GSE217735 | GEO

CROPSeq of Putative AD- and PSP-associated cis-Regulatory Regions in iPSC-derived Neurons and Microglia

Project description:We performed a pooled CRISPRi screen (CROP-seq) and genome editing to validate 19 genetic variants prioritized from massively parallel reporter assays to screen 5,706 polymorphisms from genome-wide association studies for both Alzheimer’s disease (AD) and Progressive Supranuclear Palsy (PSP) across 11 distinct loci. This allowed us to pinpoint regulatory targets in a cell-type specific manner.

2022-07-05 | GSE207099 | GEO

Genome-wide CRISPRi screen for myriocin sensitivity

Project description:To delineate cellular pathways underlying cell growth in the absence of sphingolipid syntehsis, we performed a genome-wide CRISPRi screen to identify genetic modifiers of myriocin sensitivity in human K562 cells.

2020-07-09 | GSE154045 | GEO

Landscape of enhancer disruption and functional screen in melanoma [HiChIP]

Project description:The high mutation rate across the whole melanoma genome provides a major challenge in stratifying true driver events from the background mutations. Many non-coding recurrent events, such as those occurred in enhancer, can shape tumor evolution, emphasizing the importance in systematically deciphering enhancer disruptions in melanoma. Here, we leveraged 297 melanoma whole-genome sequencing (WGS) samples to prioritize highly recurrent regions (HRRs). By performing a genome-scale CRISPR interference (CRISPRi) screen on HRR-associated enhancers in melanoma cells, we identified 66 significant hits which could have tumor-suppressive roles. These functional enhancers show unique mutational patterns independent of classical significantly mutated genes in melanoma. Target gene analysis for the essential enhancers revealed many known and hidden mechanisms underlying melanoma development. We demonstrated that a super enhancer element could modulate melanoma cell proliferation by targeting MEF2A and another distal enhancer was able to sustain PTEN tumor-suppressive potential via long-range interaction. Our study established a catalogue of crucial enhancers and their target genes in melanoma development and progression, which illuminates the identification of novel mechanism of dysregulation for melanoma driver genes and new therapeutic targeting strategy.

2023-10-11 | GSE210423 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data