Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide KO CRISPR-Cas9 screen on Haploid human embryonic stem cells with TP53 or MLH1 LoF

ABSTRACT: Haploid human embryonic stem cells harboring TP53 or MLH1 knockout (KO) were subjected to a genome-wide CRISPR-Cas9 knockout screen to identify synthetic lethal interactions associated with the mentioned genes.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Homo sapiens

SUBMITTER: Hagit Philip

PROVIDER: E-MTAB-13682 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A secondary, tailored CRISPR-Cas9 knockout library targeting the specified genes was identified through the TP53 knockout genome-wide screen

Project description:A secondary custom CRISPR-Cas9 screen, encompassing the 132 genes identified in the genome-wide TP53 knockout screen along with additional 93 genes serving as positive and negative controls.

2025-12-13 | E-MTAB-13685 | biostudies-arrayexpress

Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq

Project description:Multi-modal profiling of different molecular layers from the same single cell enables more comprehensive characterisations of cellular heterogeneity compared to conventional single-modality approaches. A key example is co-detection of chromatin accessibility and gene expression that offers the opportunity to investigate the cell type-resolved gene regulatory mechanisms. Here, we described a sensitive and robust protocol of in situ SHERRY after ATAC-seq (ISSAAC-seq) for the concurrent measurement of chromatin accessibility and gene expression from the same single nucleus. The method begins with dual Tn5 tagging of open chromatin regions and DNA/RNA hybrid after reverse transcription that take place in bulk nuclei. Then various single-nucleus isolation strategies can be used based on the experimental purpose of the user. The protocol is highly modular with flexible throughputs ranging from several hundreds to tens of thousands of nuclei. The generated data are of high quality in both modalities. The entire workflow can be finished within 1 or 2 days, and the procedures works on multiple different platforms.

2025-06-01 | E-MTAB-15131 | biostudies-arrayexpress

CUT&Tag chromatin profiling of H2AK119Ub, H3K27me3, H3K27ac and H3K4me3 histone in MC38 colon carcinoma cell line

Project description:The deubiquitinating enzyme BAP1 can remove the ubiquitination modification of H2AK119. To reveal the mechanism by which Bap1 deletion in MC38 colon carcinoma cell line causes an anti-tumor immune response from the epigenetic level, we generated CUT&Tag data of H2AK119Ub, H3K27me3, H3K27ac and H3K4me3 histone in MC38-Bap1-Wildtype and MC38-Bap1-Knockout isolated from Rag2-deficient mice.

2025-07-06 | E-MTAB-10585 | biostudies-arrayexpress

Single-cell RNA-sequencing of mouse thymic epithelial cells across the first year of life

Project description:The thymus shapes the T cell receptor repertoire, and is one of the first organs to rapidly age, with gross changes in cellularity and architecture. To resolve the nature of these changes we used SMART-Seq2 on FACS purified thymic epithelial cells (TEC) across the first year of mouse life. We sorted 4 TEC populations in each of 5 mice at each age (1 week, 4 weeks, 16 weeks, 32 weeks and 52 weeks old).

2020-09-14 | E-MTAB-8560 | biostudies-arrayexpress

Proteomic Analysis of Protein Methylation in the Yeast Saccharomyces cerevisiae

Project description:Protein methylation catalyzed by SAM-dependent methyltransferase represents a major PTM involved in important biological processes. Because methylation can occur on nitrogen, oxygen and sulfur centers and multiple methylation states exist on the nitrogen centers, methylproteome remains poorly documented. Here we present the methylation by isotope labeled SAM (MILS) strategy for a highly-confident analysis of the methylproteome of the SAM-auxotrophic Saccharomyces cerevisiae based on the online multidimensional μHPLC/MS/MS technology. We identified 117 methylated proteins, containing 182 methylation events associated with 174 methylation sites. About 90% of these methylation events were previously unknown. Our results indicated, 1) over 6% of the yeast proteome are methylated, 2) the amino acid residue preference of protein methylation follows the order Lys >> Arg > Asp > Glu ≈ Gln ≈ Asp > His > Cys, 3) the methylation state on nitrogen center is largely exclusive, and 4) the methylated proteins are located mainly in nucleus/ribosome associated with translation/transcription and DNA/RNA processing. Our dataset is the most comprehensive methylproteome known-to-date of all living organisms, and should significantly contribute to the field of protein methylation and related research.

2020-01-27 | PXD000606 | Pride

Single-cell RNA sequencing of germ-free zebrafish embryos

Project description:The present study was conducted in the frame of the EU-funded Graphene Flagship project. We previously evaluated the impact of graphene oxide (GO) on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild-type versus AhR-deficient zebrafish. Here, we performed single-cell RNA-sequencing (10x Genomics) on whole (dissociated) germ-free (GF) zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.

2022-07-22 | E-MTAB-11984 | biostudies-arrayexpress

Single-cell RNA sequencing of lck-GFP transgenic zebrafish

Project description:The present study was conducted in the frame of the EU-funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide (GO) on the (innate) immune system using zebrafish as a model. We previously performed single-cell RNA-sequencing of germ-free zebrafish embryos exposed to GO plus the microbial metabolite butyrate (BA). Here, we performed a follow up experiment using germ-free lck-GFP transgenic fish in which the zebrafish were exposed to GO plus BA at 5 dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single-cell RNA-sequencing using 10x Genomics.

2022-07-23 | E-MTAB-11991 | biostudies-arrayexpress

Single Cell Multi-Omics Profiling Using ISSAAC-seq

Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.

2022-06-15 | E-MTAB-11264 | biostudies-arrayexpress

Single-cell RNA-sequencing of spinal cord ependymal cells from FOXJ1-EGFP mice

Project description:The spinal cord neural stem cell potential is contained within the ependymal cells lining the central canal. Ependymal cells are, however, heterogeneous and we know little about what this reflects. To gain new insights into ependymal cell heterogeneity, we microdissected the ependymal cell layer from the thoracic spinal cord of 4 FOXJ1-EGFP transgenic mice (2.5-to-3-month old). After after dissociating the tissue into a cell suspension, we sorted single GFP-positive ependymal cells into lysis plates. cDNA synthesis was performed using Smart-seq2 technology.

2022-12-13 | E-MTAB-11563 | biostudies-arrayexpress

A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle

Project description:Single cell or single nuclei RNA sequencing of mixed HEK 293 and 3T3 populations using the Nadia droplet sequencing platform. Samples cover different numbers of beads from which cDNA libraries were prepared.

2021-04-10 | E-MTAB-10296 | biostudies-arrayexpress

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