Ontology highlight
ABSTRACT:
PROVIDER: PRJNA603280 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10969376_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR10969377_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR10969378_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR10969379_subreads.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:<p>Due to the paucity of patient derived models in rare cancers, identification of therapeutic targets remains challenging. We developed a patient derived model, CLF-PED-015-T, from a patient with an undifferentiated sarcoma. From this model, we performed pooled RNAi and CRISPR-Cas9 negative selection screens and integrated that with a small molecule screen. Integration of these data identified CDK4 and XPO1 as potential therapeutic targets.</p>
| phs001121 | dbGaP
Project description:Pioneer transcription factors, by interacting with nucleosomes, scan silent, compact chromatin to target regulatory sequences, enabling cooperative binding events that modulate local chromatin structure and gene activity. However, not all cognate motifs are targeted by pioneer factors and dynamic scanning parameters required to scan compact chromatin are unknown. A combined genomics and single-molecule tracking approach shows that to target DNase-resistant, low-histone turnover sites, pioneer factors FOXA1 and SOX2 display opposite dynamics of chromatin scanning: slow, with low nucleoplasmic diffusion and stable interactions, versus fast, with high nucleoplasmic diffusion and transient interactions, respectively. Despite such differences, the ability of FOXA1 and SOX2 to scan low-mobility chromatin, mediated by protein domains outside of the respective DNA binding domains, leads to targeting silent chromatin. By contrast, non-pioneer HNF4A predominantly targets DNase-sensitive, nucleosome-depleted regions. We conclude that the targeting of compact chromatin sites by pioneer factors can be performed through diverse dynamic processes. Micrococcol nuclease digestion and sequencing (MNase-seq) of human BJ fibroblasts
2023-06-07 | GSE220569 | GEO
Project description:Summary statistics for Malaria Genomic Epidemiology Network, "A novel locus of resistance to severe malaria in a region of ancient balancing selection", Nature (2015)
| EGAD00010001081 | EGA
Project description:Pioneer transcription factors, by interacting with nucleosomes, scan silent, compact chromatin to target regulatory sequences, enabling cooperative binding events that modulate local chromatin structure and gene activity. However, not all cognate motifs are targeted by pioneer factors and dynamic scanning parameters required to scan compact chromatin are unknown. A combined genomics and single-molecule tracking approach shows that to target DNase-resistant, low-histone turnover sites, pioneer factors FOXA1 and SOX2 display opposite dynamics of chromatin scanning: slow, with low nucleoplasmic diffusion and stable interactions, versus fast, with high nucleoplasmic diffusion and transient interactions, respectively. Despite such differences, the ability of FOXA1 and SOX2 to scan low-mobility chromatin, mediated by protein domains outside of the respective DNA binding domains, leads to targeting silent chromatin. By contrast, non-pioneer HNF4A predominantly targets DNase-sensitive, nucleosome-depleted regions. We conclude that the targeting of compact chromatin sites by pioneer factors can be performed through diverse dynamic processes. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HNF4A, FOXA1, FOXA1-DBD, FOXA1-NHAA, FOXA1-RRAA, as well as H2B-HALO after ectopic expression in human BJ fibroblast cells.
2023-06-07 | GSE220567 | GEO
Project description:We have previously observed that regulatory B cells expressing the apoptosis-inducing surface molecule Fas ligand were enriched in the B cell fraction denoted by a surface phenotype of CD5+CD1dhigh. To identify potential growth factors, transcriptional regulators, or surface markers that might better characterize regulatory B cells, we compared global gene expression by microarray in two B cells subsets isolated by FACS. Splenocytes from 20 DBA/1 male mice were harvested, pooled, and CD19+ B cells were isolated by positive selection using MACS. B cells were then stained for CD5 and CD1d and sorted by FACS into CD5+CD1dhigh and CD5-CD1dhigh populations. Single replicates of both CD5+CD1dhigh and CD5-CD1dhigh B cells from pooled mouse splenocytes were isolated and assay using the Affymetrix GeneChip Mouse 430 2.0 Array.
2013-06-30 | E-GEOD-46245 | biostudies-arrayexpress
Project description:Nicotiana benthamiana was infected with several strains of grapevine fanleaf virus (GFLV). Apical tissue was collected 4, 7, and 12 days after inoculation, with identical samples for shotgun proteomics and transcriptomics analysis. Five leaf discs per leaf were collected a pooled by three plants into a single tube at each time point. Five biological replicates represent each treatment at each time point for a total of 75 samples. Two samples were lost between sample processing and data acquisition. The analysis methods between proteomics and transcriptomics were then cross-analyzed for host genes responsible for phenotypic differences upon infection.
2023-07-20 | PXD037185 | Pride
Project description:We developed SCAN-seq2, a high-throughput and highly sensitive single-cell RNA sequencing method based on the TGS platform. Our study demonstrated that SCAN-seq2 improves upon the previous method, SCAN-seq, in terms of sensitivity and throughput. By using reference-guided assembly of single-cell data, we were able to identify thousands of novel full-length RNA isoforms, including cell type-specific expression patterns of pseudogenes. We also accurately determined V(D)J rearrangement events in T and B cells. Lastly, we found that treatment of HepG2 and Hela cells with the spliceosome inhibitor Isoginkgetin (IGG) resulted in a subpopulation of cells with distinct apoptosis features. Our study provides a promising new tool for single-cell transcriptome research. The source code for SCAN-seq2 data analysis pipelines is available at https://github.com/liuzhenyu-yyy/SCAN-seq2 .
2022-11-15 | GSE203561 | GEO