Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genetic dependencies associated with transcription factor activities in human cancer cell lines [SLAM-seq]

ABSTRACT: Genetic dependencies associated with transcription factor activities in human cancer cell lines [SLAM-seq]

PROVIDER: PRJNA1071713 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR27822177.fastq.gz	Fastqsanger.gz
	SRR27822178.fastq.gz	Fastqsanger.gz
	SRR27822179.fastq.gz	Fastqsanger.gz
	SRR27822180.fastq.gz	Fastqsanger.gz
	SRR27822181.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 17

Similar Datasets

Genetic dependencies associated with transcription factor activities in human cancer cell lines

Project description:Genetic dependencies associated with transcription factor activities in human cancer cell lines

| PRJNA1099147 | ENA

Genetic dependencies associated with transcription factor activities in human cancer cell lines [SLAM-seq]

Project description:Transcription factors (TFs) are important mediators of aberrant transcriptional programs in cancer cells. In this study, we focused on TF activity (TFa) as a new biomarker for cell line-selective anti-proliferative effects, in that high TFa predicts sensitivity to loss-of-function of a given gene (i.e., genetic dependencies (GD)). Our linear regression-based framework identified 3,043 pan-cancer and 3,952 cancer-type-specific candidate TFa-GD associations from cell line data, which were then cross-examined for impact on survival in patient data. One of the most prominent biomarkers was TEAD1 activity, whose associations with its predicted GDs were validated through experimental evidence as proof of concept. Overall, these TFa-GD pairs represent an attractive resource for identifying innovative, biomarker-driven hypotheses for drug discovery programs in oncology.

2024-04-29 | GSE254799 | GEO

Genetic dependencies associated with transcription factor activities in human cancer cell lines [CROP-seq]

Project description:Genetic dependencies associated with transcription factor activities in human cancer cell lines [CROP-seq]

| PRJNA1099153 | ENA

Genetic dependencies associated with transcription factor activities in human cancer cell lines [CROP-seq]

Project description:Transcription factors (TFs) are important mediators of aberrant transcriptional programs in cancer cells. In this study, we focused on TF activity (TFa) as a new biomarker for cell line-selective anti-proliferative effects, in that high TFa predicts sensitivity to loss-of-function of a given gene (i.e., genetic dependencies (GD)). Our linear regression-based framework identified 3,047 pan-cancer and 3,952 cancer-typespecific candidate TFa-GD associations from cell line data, which were then crossexamined for impact on survival in patient cohorts. One of the most prominent biomarkers was TEAD1 activity, whose associations with its predicted GDs were validated through experimental evidence as proof of concept. Overall, these TFa-GD associations represent an attractive resource for identifying innovative, biomarkerdriven hypotheses for drug discovery programs in oncology.

2024-04-29 | GSE263747 | GEO

Genetic dependencies associated with transcription factor activities in human cancer cell lines

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

2024-04-29 | GSE263748 | GEO

Mapping the landscape of genetic dependencies in chordoma

Project description:Identifying the spectrum of genes required for cancer cell survival can reveal essential cancer circuitry and therapeutic targets, but such a map remains incomplete for many cancer types. We apply genome-scale CRISPR-Cas9 loss-of-function screens to map the landscape of selectively essential genes in chordoma, a bone cancer with few validated targets. This approach confirms a known chordoma dependency, TBXT (T; brachyury), and identifies a range of additional dependencies, including PTPN11, ADAR, PRKRA, LUC7L2, SRRM2, SLC2A1, SLC7A5, FANCM, and THAP1. CDK6, SOX9, and EGFR, genes previously implicated in chordoma biology, are also recovered. We find genomic and transcriptomic features that predict specific dependencies, including interferon-stimulated gene expression, which correlates with ADAR dependence and is elevated in chordoma. Validating the therapeutic relevance of dependencies, small-molecule inhibitors of SHP2, encoded by PTPN11, have potent preclinical efficacy against chordoma. Our results generate an emerging map of chordoma dependencies to enable biological and therapeutic hypotheses.

2023-03-09 | GSE226734 | GEO

Tracking adipose-tissue Treg provenance, dependencies, and activities via T cell receptor transgenic mice

Project description:Tracking adipose-tissue Treg provenance, dependencies, and activities via T cell receptor transgenic mice

| PRJNA451105 | ENA

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

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

2024-10-01 | GSE231286 | GEO

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

SLAM-seq ML-792

Project description:SLAM-seq ML-792