11791 results for "cancer rna-seq"

in 11.68 milliseconds.

• PD1-targeted delivery of an IL-2 variant induces a multifaceted anti-tumoral T cell response in human lung cancer

  To explore PD1-IL2v-specific effects on CD8 and CD4 T cells at a transcriptomic level, we performed single-cell RNA sequencing of patient-derived tumor fragments (PDTFs) which were treated with either Isotype (DP47), Isotype-IL2v (DP47-IL2v), anti-PD1 (PembroPGLALA) or PD1-IL2v (PembroPGLALA-IL2v) for 48 hours.

  Study EGAS50000000396

• RNA and whole-exome sequencing of 22 patients with non-small cell lung cancer

  Whole exome sequencing from pre-treatment samples and matched blood normals from 22 patients. Of these individuals, on-treatment samples are available for a subset of 18 patients. RNA sequencing from pre-treatment samples from 21 patients. Of these individuals, on-treatment samples are available for a subset of 15 patients.

  Dataset EGAD00001008733

• Cellular Indexing of Transcriptomes and Epitopes Sequencing (CITE-Seq) Analysis to Investigate the Impact of Granulocyte-Colony Stimulating Factor on CRISPR/Cas9 Gene Edited Human Hematopoietic Stem Cell Function

  Our research using in-vivo preclinical xenograft mouse models demonstrated that G-CSF impedes engraftment of CRISPR-Cas9 gene edited human hematopoietic stem cells (HSCs). In this CITE-seq study, we sought to investigate the mechanisms by which G-CSF negatively impacts long-term repopulating functions of CRISPR-Cas9 gene edited human HSCs. Accordingly, human CD34+ cells were obtained from a healthy volunteer and edited with Cas9 alone (Cas9 group), Cas9+AAVS1-targeting gRNA (RNP group), or Cas9+AAVS1-targeting gRNA+GSE56 (RNP/GSE56 group). Then, these edited cells were transplanted into busulfan-conditioned NSG mice, and these mice subsequently received 3 days of phosphate buffered saline (PBS) or G-CSF. Each mouse was subsequently euthanized and harvested for bone marrow cells and human CD34+cells were isolated using immunomagnetic beads. Isolated CD34+ cells from a total of 6 mice were individually stained with Total seq B CITE-seq antibodies (CD38, CD45RA, CD90, CD49f) + hashtag oligo antibodies 1, 2, 3, 4, 5 and 6. Fluorescence activated cell sorting (FACS) was used to purify ~2,500 cells from each group that were subsequently pooled for CITE-seq library preparation and sequencing. Seurat was used to demultiplex data into 6 individual groups and differential gene expression analysis was performed to evaluate the impact of G-CSF within Cas9, RNP and RNP/GSE56 groups.

  Study phs003277

• Korean Advanced Thyroid Cancer Dataset

  Massively-parallel DNA sequencing of 113 advanced thyroid cancers and Massively-parallel RNA sequencing of 25 advanced thyroid cancers

  Dataset EGAD00001004845

• RNAseq of resident memory T cells from human lung tumor

  This dataset includes the RNA sequencing of 14 samples. Samples are FACS sorted CD8+ T cells expressing or not the integrin CD103. The paired samples (TRM and non-TRM) were sorted from the tumor of 7 lung cancer patients.

  Dataset EGAD00001006812

• Sequencing data for oesophageal and related samples - Katz-Summercorn, Jammula et al (RNA)

  Data supporting: “Multi-omic cross-sectional cohort study of pre-malignant Barrett’s esophagus reveals structural variation and retrotransposon activity occur early in cancer evolution.” Katz-Summercorn, Jammula et al. RNAseq (BAM files)

  Dataset EGAD00001006353

• Single cell RNA sequencing of colorectal cancer patients (KUL5)

  All libraries were sequenced on Illumina NextSeq or NovaSeq6000 until sufficient saturation was reached.

  Dataset EGAD00001008585

• Long Read sequencing data from 4 tumor/germline samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). Additionally, tumor/germline samples from 4 patients were sequenced using Oxford Nanopore technology. This dataset contains 8 BAM files corresponding to the Long read sequencing data.

  Dataset EGAD50000000731

• Knoll et al Identification of drug candidates targeting monocyte reprogramming in people living with HIV

  Introduction People living with HIV (PLHIV) are characterized by functional reprogramming of innate immune cells even after long-term antiretroviral therapy (ART). In order to assess technical feasibility of omics technologies for application to larger cohorts, we compared multiple omics layers. Methods Bulk and single-cell transcriptomics, flow cytometry, proteomics, chromatin landscape analysis by ATAC-seq as well as ex vivo drug stimulation was performed in a small number of blood samples derived from PLHIV and healthy controls from the 200-HIV cohort study. Results Single-cell RNA-seq analysis revealed that most immune cells in peripheral blood of PLHIV are altered in their transcriptomes and that a specific functional monocyte state previously described in acute HIV infection is still existing in PLHIV while other monocyte cell states are only occurring acute infection. Moreover, a reverse transcriptome approach on a rather small number of PLHIV was sufficient to identify drug candidates for reversing the transcriptional phenotype of monocytes in PLHIV. Discussion These scientific findings and technological advancements for clinical application of single-cell transcriptomics form the basis for the larger 2000-HIV multicenter cohort study on PLHIV, for which a combination of bulk and single-cell transcriptomics will be included as the leading technology to determine disease endotypes in PLHIV and to predict disease trajectories and outcomes.

  Study EGAS00001007460

• Epigenomics of Human CD8 T cell Differentiation and Aging

  The efficacy of the adaptive immune response declines dramatically with age, but the cell-intrinsic mechanisms driving the changes characteristic of immune aging in humans remain poorly understood. One hallmark of immune aging is the loss of self-renewing naive cells and the accumulation of differentiated but dysfunctional cells within the CD8 T cell compartment. Using ATAC-seq, we first inferred the transcription factor binding activities that maintain the naive and central and effector memory CD8 T cell states in young adults. Integrating our results with RNA-seq, we determined that BATF, ETS1, Eomes, and Sp1 govern transcription networks associated with specific CD8 T cell subset properties, including activation and proliferative potential. Extending our analysis to aged humans, we found that the differences between memory and naive CD8 T cells were largely preserved across age, but that naive and central memory cells from older individuals exhibited a shift toward a more differentiated pattern of chromatin openness. Additionally, aged naive cells displayed a loss in chromatin openness at gene promoters, a phenomenon that appears to be due largely to a loss in binding by NRF1, leading to a marked drop-off in the ability of the naive cell to initiate transcription of mitochondrial genes. Our findings identify BATF- and NRF1-driven gene regulation as targets for delaying CD8 T cell aging and restoring T cell function.

  Study phs001187