3659 results for "RNA AND sequencing OR transcriptome"

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• Single cell RNA sequencing of peripheral blood HSPC from patients with sickle cell anemia and healthy donors

  Neutrophils and monocytes are critical contributors to the pathophysiology of sickle cell anemia (SCA) and are persistently elevated in patients' circulation. While chronic hemolysis has been implicated in this leukocytosis, the underlying mechanisms remain incompletely understood. Our data show a myeloid-skewed transcriptional signature in early progenitor populations, including multipotent progenitors (MPPs) and hematopoietic stem cells (HSCs). Notably, we identify upregulation of the type I interferon signaling pathway in HSPCs as a key driver of early myeloid programming in SCA.

  Study EGAS50000001046

• Bulk RNA sequencing of metastatic colorectal cancer patient-derived xenografts with known response to irinotecan

  Chemotherapy is the standard-of-care treatment for metastatic colorectal cancer (mCRC) and benefits some patients, but what distinguishes responders from non-responders is unclear. In this study, we expand a pre-existing collection (https://doi.org/10.1158/2159-8290.CD-24-0556) of molecularly annotated patient-derived xenografts to uncover functional predictors of response to 5-FU and irinotecan combination therapy (FOLFIRI) in mCRC. We complemented previous expression profiles with bulk RNAseq for 38 xenografts with known response to irinotecan.

  Study EGAS50000001485

• Blood neutrophils in COPD derive from activated progenitors in the bone marrow

  Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small airway inflammation, emphysema and severe breathing difficulties. Low-grade systemic inflammation is an established hallmark of severe disease, however, the molecular changes in peripheral immune cells remain far from understood. We combined multi-color flow cytometry with single-cell RNA sequencing and showed that blood neutrophil numbers are significantly increased in COPD and they are a heterogeneous population. A transcriptomic state that expressed interferon response genes correlated with alveolar damage and acute exacerbations. Furthermore, bronchoalveolar neutrophils expressed gene signatures corresponding to certain blood neutrophil states. Last, our data in a murine model of cigarette smoke exposure demonstrated that bone marrow neutrophil progenitors are expanded in smoke-treated animals and display signs of immune activation. Our study provides evidence that COPD systemic inflammation may derive from an activated haematopoietic precursor compartment.

  Dataset EGAD00001008788

• Blood neutrophils in COPD derive from activated progenitors in the bone marrow sc Seqwell

  Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small airway inflammation, emphysema and severe breathing difficulties. Low-grade systemic inflammation is an established hallmark of severe disease, however, the molecular changes in peripheral immune cells remain far from understood. We combined multi-color flow cytometry with single-cell RNA sequencing and showed that blood neutrophil numbers are significantly increased in COPD and they are a heterogeneous population. A transcriptomic state that expressed interferon response genes correlated with alveolar damage and acute exacerbations. Furthermore, bronchoalveolar neutrophils expressed gene signatures corresponding to certain blood neutrophil states. Last, our data in a murine model of cigarette smoke exposure demonstrated that bone marrow neutrophil progenitors are expanded in smoke-treated animals and display signs of immune activation. Our study provides evidence that COPD systemic inflammation may derive from an activated haematopoietic precursor compartment.

  Dataset EGAD00001008908

• Single-cell RNA sequencing data of human lymph node samples generated with BD Rhapsody

  The single cell data were generated based on four cartridges. The samples are multiplexed: 0. Sample Run Id Hash Gender Age 1. FL-6 Run1_C1 4 f 71 2. rLN-3 Run1_C1 6 f 72 3. DLBCL-4 Run1_C1 7 f 68 4. DLBCL-1 Run1_C1 8 m 66 5. FL-4 Run1_C1 9 m 41 6. DLBCL-3 Run1_C2 10 f 60 7. rLN-4 Run1_C2 11 f 58 8. rLN-5 Run1_C2 12 m 61 9. FL-1 Run2_C1 1 f 81 10. DLBCL-2 Run2_C1 2 m 80 11. rLN-2 Run2_C1 3 f 42 12. FL-5 Run2_C1 4 m 66 13. DLBCL-8 Run2_C1 5 m 64 14. DLBCL-6 Run2_C2 6 m 76 15. rLN-1 Run2_C2 7 m 39 16. FL-3 Run2_C2 8 f 76 17. DLBCL-5 Run2_C2 9 m 66 18. FL-2 Run2_C2 10 f 58 19. DLBCL-7 Run2_C2 11 f 71

  Dataset EGAD00001010044

• Blood neutrophils in COPD derive from activated progenitors in the bone marrow sc Rhapsody

  Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small airway inflammation, emphysema and severe breathing difficulties. Low-grade systemic inflammation is an established hallmark of severe disease, however, the molecular changes in peripheral immune cells remain far from understood. We combined multi-color flow cytometry with single-cell RNA sequencing and showed that blood neutrophil numbers are significantly increased in COPD and they are a heterogeneous population. A transcriptomic state that expressed interferon response genes correlated with alveolar damage and acute exacerbations. Furthermore, bronchoalveolar neutrophils expressed gene signatures corresponding to certain blood neutrophil states. Last, our data in a murine model of cigarette smoke exposure demonstrated that bone marrow neutrophil progenitors are expanded in smoke-treated animals and display signs of immune activation. Our study provides evidence that COPD systemic inflammation may derive from an activated haematopoietic precursor compartment.

  Dataset EGAD00001009704

• Massive parallel RNA sequencing of highly purified mesenchymal cells derived from bone marrow specimens of 45 low-risk myelodysplastic syndrome cases

  Highly purified mesenchymal cells (CD45-/7AAD-/CD235a-/CD31-/CD271+/CD105+) were prospectively FACS-isolated from bone marrow specimens of 45 low-risk myelodysplastic syndrome (LRMDS) cases. Gene expression profiles (GEPs) of the 45 LRMDS have been compared to GEPs derived from likewise highly purified mesenchymal cells obtained from bone marrow specimens of healthy donors for the identification of inflammatory signatures. Additionally, an overlap in inflammatory signatures has been determined by comparing the GEPs of these 45 LRMDS cases to the GEPs of 4 Shwachman-Diamond syndrome and 3 Diamond-Blackfan anemia cases, both representing different subclasses of congenital pre-leukemia syndromes with a tendency of leukemic progression and perturbed niche compartment. Finally, the GEPs and gene expression signatures have been utilized for prognostication and the prediction of leukemic progression.

  Dataset EGAD00001002658

• Identification of Novel Immunotherapy Targets in Myeloma

  RNA sequencing (RNA-Seq) was performed on 94 multiple myeloma (MM) patient samples. We used genomic subgroup and high-risk markers to identify therapeutic targets, including TNFRSF17, GPRC5D, ITGA4, and LAX1, with low predicted toxicity and high specificity to MM and genomic subgroups such as those with TP53 alterations.

  Study phs003772

• 41 fibroblast RNAseq samples of pediatric patients with childhood epilepsy and developmental delay

  We used RNA sequencing of patient fibroblasts to find a genetic diagnosis in patients with exome-negative childhood epilepsy. RNA extracted from 41 individuals' cultured fibroblasts (passage 3-6) was collected and sequenced at a depth of 90-110 paired reads per sample.

  Study EGAS50000000792

• Primary_DIPG_expression_profiles

  In this study, we used RNA-sequencing gene expression profiling in order to characterize specific phenotypic traits in DIPG. Seventeen primary tumor samples stereotactically biopsied at diagnosis by neurosurgeons in the Necker-Enfants Malades hospital (Paris, France) and snap-frozen for RNA extraction and subsequent poly-A mRNA purification.

  Study EGAS00001007181