Multiplexed Single Cell gene expression profile of barcoded SUM159PT cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Homo sapiens
SUBMITTER: Francesca Nadalin
PROVIDER: E-MTAB-13066 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Cancer is a heterogeneous disease, where multiple, phenotypically distinct subpopulations co-exist. Tumour evolution is a result of a complex interplay of genetic and epigenetic factors. To predict the molecular drivers of distinct cancer responses, we apply single-cell lineage tracing (scRNA-Seq of barcoded cells) on a triple-negative breast cancer model. SUM159PT cells infected with a lentiviral barcode library (Perturb-seq Library) were sorted according to the presence of BFP signal, treated or not with paclitaxel (PTX), and then processed by scRNA-Seq or Multiome.
2024-05-24 | E-MTAB-13064 | biostudies-arrayexpress
Project description:Pancreatic cancer is a complex disease with a desmoplastic stroma, extreme hypoxia, and inherent resistance to therapy. Understanding the signaling and adaptive response of such an aggressive cancer is key to making advances in therapeutic efficacy and understanding disease progression. Redox factor-1 (Ref-1), a redox signaling protein, regulates the DNA binding activity of several transcription factors, including HIF-1. The conversion of HIF-1 from an oxidized to reduced state leads to enhancement of its DNA binding. In our previously published work, knockdown of Ref-1 under normoxia resulted in altered gene expression patterns on pathways including EIF2, protein kinase A, and mTOR. In this study, single cell RNA sequencing (scRNA-seq) and proteomics were used to explore the effects of Ref-1 on metabolic pathways under hypoxia.Results: We also integrated the scRNA data analysis with the proteomic analysis and found that the differentially expressed genes and pathways identified from the scRNA-seq data are highly consistent to the significant proteins observed in the proteomics data, especially for the upregulated cell cycle and transcription pathways and downregulated metabolic, apoptosis and signaling pathways under hypoxia. Conclusion: The scRNA-seq and proteomics data consistently demonstrated down-regulated central metabolism pathways in APE1/Ref-1 knockdown vs scrambled control under both normoxia and hypoxia conditions. Experimental Methods: scRNA-seq comparing pancreatic cancer cells expressing less than 20% of the Ref-1 protein was analyzed using left truncated mixture Gaussian model. Matched samples were also collected for bulk proteomic analysis of the four conditions. scRNA-seq data was validated using proteomics and qRT-PCR. Ref-1’s role in mitochondrial function was confirmed using mitochondrial function assays and qRT-PCR. Results: We also integrated the scRNA data analysis with the proteomic analysis and found that the differentially expressed genes and pathways identified from the scRNA-seq data are highly consistent to the significant proteins observed in the proteomics data, especially for the upregulated cell cycle and transcription pathways and downregulated metabolic, apoptosis and signaling pathways under hypoxia. Conclusion: The scRNA-seq and proteomics data consistently demonstrated down-regulated central metabolism pathways in APE1/Ref-1 knockdown vs scrambled control under both normoxia and hypoxia conditions.
2021-09-09 | PXD020515 | Pride
Project description:Baseline MDA-MB-231 TGL cells were processed by scRNA-Seq.
2024-07-22 | E-MTAB-13896 | biostudies-arrayexpress
Project description:"The main goal of the project is to develop a new generation of bioinformatics resources for the integrative analysis of multiple types of omics data. These resources include both novel statistical methodologies as well as user-friendly software implementations. STATegra methods address many aspects of the omics data integration problem such as the design of multiomics experiments, integrative transcriptional and regulatory networks, integrative variable selection, data fusion, integration of public domain data, and integrative pathway analysis. To support method development STATegra uses a model biological system, namely the differentiation process of mouse pre-B-cells. The STATegra consortium generated data focused on a critical step in the differentiation of B lymphocytes, which are key components of the adaptive immune system. Transcription factors of the Ikaros family are central to the normal differentiation of B cell progenitors and their expression increases in response to developmental stage-specific signals to terminate the proliferation of B cell progenitors and to initiate their differentiation. In particular, a novel biological system that models the transition from the pre-BI stage to the pre-BII subsequent stage, where B cell progenitors undergo growth arrest and differentiation, was used. The approach involves a pre-B cell line, B3 , and an inducible version of the Ikaros transcription factor, Ikaros-ERt2. Ikaros factors act to down-regulate genes that drive proliferation and to simultaneously up-regulate the expression of genes that promote the differentiation of B cell progenitors. Hence, in the B3 system, before induction of Ikaros, cells proliferate and their gene expression pattern is similar to proliferating B cell progenitors in vivo. Following Ikaros induction, B3 cells undergo gene expression changes that resemble those that occur in vivo during the transition from cycling to resting pre-B cells, followed by a marked reduction in cellular proliferation and by G1 arrest. On this system the consortium has created a high-quality data collection consisting of a replicated time course using seven different omics platforms: RNA-seq, miRNA-seq, ChIP-seq, DNase-seq, Methyl-seq, proteomics and metabolomics, which is used to assess and to validate STATegra methods."
2019-03-05 | PXD003263 | Pride
Project description:During development, the amniote organizer, Hensen’s node, contributes cells to the developing axis in head-to-tail direction. However, some cells remain resident in the node and it has been suggested that these resident cells are stem cells. This study aimed to characterise single resident cells and their environment within the node. Using the chick as an amniote model, we generated transcriptomes of single resident cells (scRNA-seq of GFP cells that remained resident till stage-HH8 following a GFP-donor homotopic transplant into a non-GFP host) and of six node sub-regions (bulk RNA-seq of GFP-transgenic stage-HH8 node, but otherwise un-manipulated embryos). We also obtained transcriptomes of single cells with resident behaviour that would normally never enter the node, but were made to do so (scRNA-seq of cells that remained resident till HH8 following a GFP-donor heterotopic/heterochronic transplant into a non-GFP host).
2022-02-02 | E-MTAB-11216 | biostudies-arrayexpress
Project description:During development, the amniote organizer, Hensen’s node, contributes cells to the developing axis in head-to-tail direction. However, some cells remain resident in the node and it has been suggested that these resident cells are stem cells. This study aimed to characterise single resident cells and their environment within the node. Using the chick as an amniote model, we generated transcriptomes of single resident cells (scRNA-seq of GFP cells that remained resident till stage-HH8 following a GFP-donor homotopic transplant into a non-GFP host) and of six node sub-regions (bulk RNA-seq of GFP-transgenic stage-HH8 node, but otherwise un-manipulated embryos). We also obtained transcriptomes of single cells with resident behaviour that would normally never enter the node, but were made to do so (scRNA-seq of cells that remained resident till HH8 following a GFP-donor heterotopic/heterochronic transplant into a non-GFP host).
2022-02-02 | E-MTAB-9116 | biostudies-arrayexpress
Project description:Immune aplastic anemia (AA) is a life-threatening bone marrow (BM) failure disorder driven by an autoimmune T cell attack against the hematopoietic stem and progenitor cells (HSPCs). However, the autoantigen targets and the role of other immune cells are unknown. Here, by combining scRNA+TCRαβ-seq, TCRβ-seq, flow cytometry and plasma cytokine profiling of >250 patients with AA, >250 patients with other hematological disorders and >1,000 healthy controls, we identify NK cells and CD8+ TEMRA cells expressing NK receptors with AA-associated TCRB-seq motifs as the most dysregulated immune cell populations in AA BM. Functional co-culture experiments with scRNA-TCRαβ-seq readout utilizing primary HSPCs and immune cells (in total 55 conditions) provide evidence that NK cells alone cannot kill HSPCs, but sensitize them to CD8+ T cell mediated killing. Furthermore, HSPCs induce strong activation of T cell clones with CD8+ TEMRA NK-like phenotype and AA-associated TCR motifs. To conclude, our results reveal convergent evolution of innate and adaptive immune cells in AA, where NK cells support CD8+ T cell mediated autoimmunity.
2024-12-12 | E-MTAB-13485 | biostudies-arrayexpress
Project description:In this study, we performed single-cell RNA sequencing (scRNA-seq) on MAIT cells extracted from the intestines of young and aged mice. For each age group, MAIT cells from five individual mice were pooled before sequencing.
2024-11-26 | E-MTAB-14483 | biostudies-arrayexpress
Project description:We performed single-cell RNA-seq of full, microdissected and dissociated mouse amygdala, 2h, 8h or 24h after tone-cued fear conditioning (CFC), and 2h after recall (exposure to CS only, 24h post-CFC), and naive homecage controls.
2023-01-01 | E-MTAB-12096 | biostudies-arrayexpress
Project description:Fluctuations in nutrient availability profoundly impact gene expression. Previous work revealed post-recruitment regulation of RNA Polymerase II (Pol II) during starvation and recovery in Caenorhabitis elegans, suggesting promoter-proximal pausing promotes rapid response to feeding. To test this hypothesis, we measured Pol II elongation genome-wide by two complementary approaches and analyzed elongation in conjunction with Pol II binding and expression. We confirmed bona fide pausing during starvation and also discovered Pol II docking. Pausing occurs at active stress-response genes that become down-regulated in response to feeding. In contrast M-bM-^@M-^\dockedM-bM-^@M-^] Pol II accumulates without initiating upstream of inactive growth genes that become rapidly up-regulated upon feeding. Beyond differences in function and expression, these two sets of genes have different core promoter motifs, suggesting alternative transcriptional machinery. Our work suggests that growth and stress genes are both regulated post-recruitment during starvation, but at initiation and elongation, respectively, coordinating gene expression with nutrient availability. We sequenced short, capped RNA (scRNA-seq) from N2 starved L1 C. elegans as well as a TFIIS mutant (RB2083). We also prepared scRNA-seq libraries from L1 larvae using one, two, or three of the enymes used to prepare the scRNA sequencing libraries as well as scRNA-seq libraries from Drosophila S2 cells using one or two of the enzymes. We further sequenced the 5' end of mRNA in starved C. elegans L1 larvae using the same enzymes as scRNA-seq.
2014-02-01 | E-GEOD-40161 | biostudies-arrayexpress