12221 results for "cancer rna-seq"

in 25.67 milliseconds.

• Functional single-cell characterization of immune aplastic anemia shows convergence of NK and NK-like CD8+ T cells with disease-associated TCR signature

  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 analyzing an international cohort of 156 AA patients with scRNA+TCRαβ-seq, TCRβ-seq, flow cytometry, and plasma cytokine profiling with comparisons to healthy controls and patients with other hematological disorders, we identify NK cells and CD8+ TEMRA cells expressing NK receptors with AA-associated TCRβ-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 provide evidence that NK cellscannot kill HSPCs alone, 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. Our results reveal the convergent evolution of innate and adaptive immune cells in AA, where NK cells support CD8+ T cell-mediated autoimmunity.

  Study EGAS00001007602

• Functional single-cell characterization of immune aplastic anemia shows convergence of NK and NK-like CD8+ T cells with disease-associated TCR signature

  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 analyzing an international cohort of 156 AA patients with scRNA+TCRαβ-seq, TCRβ-seq, flow cytometry, and plasma cytokine profiling with comparisons to healthy controls and patients with other hematological disorders, we identify NK cells and CD8+ TEMRA cells expressing NK receptors with AA-associated TCRβ-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 provide evidence that NK cellscannot kill HSPCs alone, 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. Our results reveal the convergent evolution of innate and adaptive immune cells in AA, where NK cells support CD8+ T cell-mediated autoimmunity.

  Study EGAS00001007604

• The immunological characterization of expanded tumor-infiltrating lymphocytes in renal cell carcinoma patients

  In this study, we comprehensively characterized the non-expanded and expanded tumor-infiltrating lymphocytes (TILs) from treatment-naïve RCC patients, as well as the corresponding “young” TILs (pre-REP TILs) and “rapidly expanded” TILs (REP TILs) following a clinical-grade TIL production protocol. From our scRNA+TCRαβ-seq and TCRβ-seq analyses, we show that the REP protocol preferentially favors the expansion CD4+ T-cells that originate from small T-cell clones in the tumor microenvironment (TME), indicating that the large, exhausted T-cell clones in the tumor do not expand during the protocol. We further identified RCC-associated TCR motifs that were validated in multiple TCRαβ-seq and scRNA+TCRαβ-seq datasets, as well as quantified the RCC-associated TCRs from the REP protocol. Overall, the T-cells carrying the RCC-associated TCRs remained high in the tumors and corresponding pre-REP TILs, but the frequency was reduced in the REP TILs. Furthermore, the overall anti-viral TCRs remained low throughout the REP protocol. Our results provide an in-depth understanding of the origin, phenotype, and specificity of the TCRs in RCC TILs.

  Study EGAS00001006952

• Acute myeloid leukemia sequencing data

  This study contains tumor DNA and RNA sequencing data for 1 AML patient

  Study EGAS00001006354

• Small RNA and MicroRNA sequencing data

  Small RNA and MicroRNA sequencing data was generated for the multiomics analysis of Eurotarget

  Dataset EGAD50000002294

• RNA-sequencing of SYSCOL colorectal adenoma-carcinoma samples

  RNA-sequencing alignment for SYSCOL colorectal adenoma-carcinoma samples

  Dataset EGAD00001003318

• HipSci - Monogenic Diabetes - RNA Sequencing - October 2016

  HipSci - Monogenic Diabetes - RNA Sequencing - October 2016

  Dataset EGAD00001003180

• HipSci - Monogenic Diabetes - RNA Sequencing - July 2017

  HipSci - Monogenic Diabetes - RNA Sequencing - July 2017

  Dataset EGAD00001003530

• HipSci - Bleeding and Platelet Disorders - RNA Sequencing - July 2017

  HipSci - Bleeding and Platelet Disorders - RNA Sequencing - July 2017

  Dataset EGAD00001003539

• HipSci - Healthy Normals - RNA Sequencing - May 2014

  HipSci - Healthy Normals - RNA Sequencing - May 2014

  Dataset EGAD00001000897

• Characterization of arrested B-lymphoid differentiation and leukemic cell states in ETV6-RUNX1-positive pediatric leukemia

  RNA was extracted from eight diagnostic ETV6-RUNX1 positive acute lymphoblastic leukemia samples collected in PAXgene blood RNA tubes using PAXgene Blood RNA kit (cat #762174, Qiagen GmbH, Hilden, Germany), following the version 2 instructions for manual purification. Samples were processed with Globin-Zero Gold rRNA Removal Kit (Illumina) and directional libraries were prepared using NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs). The library preparation and paired end (150 bp) sequencing were performed by Novogene (HK) Company Limited (Hong Kong, China) using Illumina Novaseq 6000 aiming at 70 million read pairs per sample.

  Dataset EGAD00001006406

• ATAC-seq in LCLs derived from constitutional MLH1 epimutation carriers and non-carrier relatives

  ATAC-seq performed in LCLs derived from constitutional MLH1 epimutation carriers and non-carrier relatives to profile alterations in chromatin accessibility associated with constitutional MLH1 epimutation.

  Dataset EGAD50000000714

• CIRCLE-seq of PDO

  CIRCLE-seq data of PDAC 1 patient-derived organoid (PDO) - Unmapped reads, libraries were sequenced using the Illumina NextSeq500 with the NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles), generating around 10M paired end 150bp reads per sample

  Dataset EGAD50000000281

• BLUEPRINT: WGBS-seq for monocytes and neutrophils

  WGBS-seq for monocytes and neutrophils

  Dataset EGAD00001000673

• McGill EMC Release 4 for assay "ATAC-seq"

  McGill EMC Release 4 for assay "ATAC-seq": Sequencing of transposase-accessible chromatin as described by Buenrostro et al. (Nature Methods 10, 1213?1218 (2013) doi:10.1038/nmeth.2688)

  Dataset EGAD00001001300

• single-cell ATAC-seq

  Single-cell ATAC-seq data for 5 CLL samples (2 controls, 3 tumor) of the CancerEpiSys-PRECiSe project.

  Dataset EGAD00001005965

• scDNA-seq

  Single cell DNA-seq data (CLL gene panel - Tapestri single-cell DNA CLL panel, Mission Bio)

  Dataset EGAD00001008960

• scRNA-seq of monocultures and co-cultures of PDAC-PDOs and CAFs

  scRNA-seq of monocultures and co-cultures of patient-derived PDAC organoids and matched CAFs. 3 sample sets per patient.

  Dataset EGAD00001009655

• Single-Cell Analysis of Human Adipogenesis

  The data in this study consists of RNA sequencing reads and read counts from single-cell and single-nuclei RNA sequencing experiments performed on two cell lines to investigate the transcriptional landscape of human adipogenesis in both the brown and white adipose tissue lineage. The two cell lines are human preadipocytes collected and isolated from a defined anatomical location in the neck of a single individual. This depot is known to harbor white adipose tissue (WAT) and brown adipose tissue (BAT). These white and brown preadipocytes were immortalized for the purposes of studying human adipogenesis in vitro. In this study we induced differentiation of these two preadipocyte lines and performed RNA sequencing on over 135,000 single cells spanning a 20-day time course from unperturbed preadipocytes to mature adipocytes from both brown and white lineages. Additionally, we performed both single-cell and single-nuclei RNA sequencing to comprehensively compare the advantages and disadvantages of either technique.

  Study phs002461

• Clear cell sarcoma sequencing data

  This study shares DNA and RNA sequencing data from Clear cell sarcoma patients

  Study EGAS00001006072

• HipSci - Bardet-Biedl Syndrome - RNA Sequencing - October 2016

  HipSci - Bardet-Biedl Syndrome - RNA Sequencing - October 2016

  Dataset EGAD00001003181

• HipSci - Bardet-Biedl Syndrome - RNA Sequencing - July 2017

  HipSci - Bardet-Biedl Syndrome - RNA Sequencing - July 2017

  Dataset EGAD00001003531

• RNA sequencing data to study "A biobank of patient-derived pediatric braintumor models"

  RNA sequencing data for the PDOX model EPD-613FH

  Dataset EGAD00001003573

• RNA sequencing of ALAL patients

  Transcriptomic data generated by RNA sequencing of 30 adults with acute leukemia of ambiguous lineage (ALAL)

  Dataset EGAD00001015547

• Dataset for cancer_of_unknown_primary-RNA

  Rare cancer sequencing data of 58 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008857