Pancreatic Differentiation Clones and Pooled Single-cell RNA-seq
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1039795 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26815437.fastq.gz | Fastqsanger.gz | |||
| SRR26815438.fastq.gz | Fastqsanger.gz | |||
| SRR26815439.fastq.gz | Fastqsanger.gz | |||
| SRR26815440.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:scRNA-seq identifies novel cell-type dependent gene functions in regulating pancreatic cell differentiation.
2024-08-22 | GSE247598 | GEO
Project description:Sequencing of pooled BAC clones from Solanum phureja doubled monoploid clone, DM1-3 516R44 (CIP801092)
| PRJEB2697 | ENA
Project description:This Series contains additional single-cell RNA-seq datasets associated with a study of how loss of epigenetic regulators, particularly ARID1A, reshapes transcriptional heterogeneity in pancreatic ductal adenocarcinoma cells. The shPseuMO-Tag system couples genetic perturbation with clonal lineage tracing. The datasets include an initial epigenetic-modifier screen, an ARID1A knockdown time course, a large-scale pooled five-shRNA experiment, acute SMARCA4 degradation, independent experiments in multiple PDAC cell lines, and matched pre-injection and lung-colonization samples. In the independent multi-cell-line experiment, BxPC3, HPAC, SW1990, and SUIT-2 were profiled using independently derived clones, whereas HPAFII was analyzed as a pooled population because stable single-cell-derived HPAFII clones could not be established.
2026-09-22 | GSE348038 | GEO
Project description:Hematopoietic stem and progenitor cells (HSPCs) balance self-renewal with on-demand differentiation of blood lineages. Modern bone marrow atlases specify static transcriptional states, but not HSPC dynamics, which are only partly understood, particularly in humans. Here, we introduce cHSPCTrack (clonal HSPC tracker), an in vitro framework for serially tracking clonal differentiation and fate acquisition from human HSPCs extracted from circulation. By following thousands of single-cell-derived clones stimulated by different cytokine combinations, cHSPCTrack reconstructs the balance between stochasticity and directed differentiation in human HSPCs. Single HSPCs stochastically yield multiple lineages under a uniform cytokine environment, with stimulatory inputs modulating differentiation probabilities by introducing biases toward preferred fates. In parallel, differentiation rates vary stochastically across and within clones. Clonal memory stabilizes the induction of a few genes per clone over otherwise archetypical differentiation trajectories. Within clones, multiple fates can interact with each other, as shown for clones mixing basophils, eosinophils, and mast cells with other fates. cHSPCTrack opens avenues for understanding hematopoietic clonal dynamics in health and disease.
2026-06-17 | GSE334867 | GEO
Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine.
2013-12-03 | GSE42449 | GEO
Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine.
2013-12-03 | GSE42452 | GEO
Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine. We extracted total RNA from 3 differentiation-defective clones, 3 good clones and 2 somatic cells, and hybridized them to Affymetrix exon arrays.
2013-12-03 | E-GEOD-42449 | biostudies-arrayexpress
Project description:Pooled TFs overexpression assay (single-cell RNAseq)
| PRJNA670898 | ENA
Project description:We have utilized advanced RNAi technology to dynamically restore endogenous PU.1 expression in p53-deficient shPU.1 AML single cell clones in vitro. This causes rapid cell cycle shutdown and reversible myeloid differentiation.
2019-05-13 | GSE76879 | GEO
Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine. We extracted total RNA from 10 hESCs and 40 hiPSCs, and hybridized them to Agilent gene expression microarrays.
2013-12-03 | E-GEOD-42452 | biostudies-arrayexpress