Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies

ABSTRACT: Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies

PROVIDER: PRJNA657290 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12455200.fastq.gz	Fastqsanger.gz
	SRR12455201.fastq.gz	Fastqsanger.gz
	SRR12455202.fastq.gz	Fastqsanger.gz
	SRR12455203.fastq.gz	Fastqsanger.gz
	SRR12455204.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 76

Similar Datasets

Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies [CRISPRseq]

Project description:Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies [CRISPRseq]

| PRJNA657266 | ENA

Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies [CRISPRseq]

Project description:Human pluripotent stem cells (hPSCs) provide an invaluable tool for modeling diseases and hold promise for regenerative medicine. For understanding pluripotency and lineage differentiation mechanisms, a critical first step involves systematically cataloging essential genes (EGs) that are indispensable for hPSC fitness, defined as cell reproduction in this study. To map essential genetic determinants of hPSC fitness, we performed genome-scale loss- of-function screens in an inducible Cas9 H1 hPSC line cultured on feeder cells and laminin to identify EGs. Among these, we found FOXH1 and VENTX, genes that encode transcription factors previously implicated in stem cell biology, as well as an uncharacterized gene, C22orf43/DRICH1. hPSC EGs are substantially different from other human model cell lines, and EGs in hPSCs are highly context dependent with respect to different growth substrates. Our CRISPR screens establish parameters for genome-wide screens in hPSCs, which will facilitate the characterization of unappreciated genetic regulators of hPSC biology.

2020-08-15 | GSE156284 | GEO

Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies

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

2020-08-15 | GSE156298 | GEO

Transcriptome profiling of H1-iCas9 cells grown on laminin and on MEFs

Project description:This experiment is part of a study of differentially essential genes in H1 hPSCs grown on different substrates ("Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies", Mair et al., Cell Reports 2018). The cells used stably express DOX-inducible Cas9 in the AAVS1 locus and were profiled together with unmodified H1 wt hPCS on both substrates to asses transcriptional changes.

2019-02-28 | GSE125509 | 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

rhizosphere substrate

Project description:rhizosphere substrate Raw sequence reads

| PRJNA1309842 | ENA

Substrate sample

Project description:Substrate soil microbial community diversity

| PRJNA593085 | ENA

substrate films

Project description:substrate films Raw sequence reads

| PRJNA792343 | ENA

Pediatric Cancer Dependencies Accelerator

Project description:Pediatric Cancer Dependencies Accelerator

| PRJNA1414614 | ENA

A genome-wide atlas of co-essential modules assigns function to uncharacterized genes

Project description:A central remaining question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into ‘co-essential’ pathways, but this approach has been limited by ubiquitous false positives. Here, we develop a statistical method that enables robust identification of gene co-essentiality and yields a genome-wide set of functional modules. This atlas recapitulates diverse pathways and protein complexes and predicts the functions of 155 uncharacterized genes. Validating top predictions, we show that TMEM189 encodes plasmanylethanolamine desaturase, the long-sought key enzyme for plasmalogen synthesis. We also show that C15orf57 binds the AP2 complex, localizes to clathrin-coated pits, and enables efficient transferrin uptake. Finally, we provide an interactive web tool for the community to explore our results. Our results establish co-essentiality profiling as a powerful resource for biological pathway identification and discovery of novel gene functions.

2022-02-16 | PXD023558 | Pride

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