9296 results for "cancer rna-seq"

in 81.55 milliseconds.

• The immunopeptidome landscape associated with T cell infiltration, inflammation and immune-editing in lung cancer

  WES sequencing of multiple regions per tumor from 8 lung cancer patients (LUSC, LCNEC and LUAD) and adjacent healthy lung tissue for each patient.

  Dataset EGAD00001008950

• Single-cell transcriptome of T-ALL P1

  In this study, we profiled single-cell transcriptome (10X genomics) of Patient-derived xenografts (PDX) T-ALL replase samples from P1 patient. Primary human T-ALL cells were recovered from cryopreserved bone marrow aspirates of patients enrolled in the ALL-BFM 2009 study. Patient-derived xenografts (PDX) were generated as previously described by intrafemoral injection of 1 Million viable primary ALL cells in NSG mice110 PDX-derived (P1)28 cells were frozen until processing. For scRNA-seq library preparation, cryopreserved cells were thawed rapidly at 37 ℃ and resuspended in 10 ml warm Roswell Park Memorial Institute (RPMI) medium with 100 μg/ml Dnase I. Cells were centrifuged for 5 mins at 300 g, and resuspended in ice-cold phosphate buffered saline (PBS) with 2% foetal bovine serum (FBS) and 5mM EDTA. Cells were stained on ice with anti-murine-CD45-PE (mCD45)(clone 30-F11; BioLegend; 1:20) in the dark for 30 mins. 1:100 DAPI was added and incubated in the dark for 5 mins before sorting. Triple negative cells (DAPI-mCD45-GFP-) were sorted (Fig. S27) using a BD FACSAria™ Fusion Cell Sorter into ice cold 0.03% bovine serum albumin (BSA) in PBS. All isolated cells were immediately used for scRNA-seq libraries, which were generated as per the standard 10x Genomics Chromium 3′ (v.3.1 Chemistry) protocol. Completed libraries were sequenced on a NextSeq5000 sequencer (HIGH-mode, 75 bp paired-end).

  Dataset EGAD00001008325

• Multimodal Profiling of 500,000 Memory T Cells from a Tuberculosis Cohort Identifies Cell State Associations with Demographics, Environment, and Disease

  We conducted CITE-seq to measure whole transcriptome gene expression and surface expression of 31 proteins. We assayed >500K memory T cells from 259 donors from a tuberculosis progression cohort (128 cases: former progressors and 131 controls: non-progresssors/latent infection) >4 years post-infection after returning to immune steady state. We defined 31 memory T cell states influenced by age, sex, genetic ancestry, and season. After correcting for these covariates, we found that one cell state (C-12), resembling the T helper cells Th17s, were depleted in cases compared to controls. When sorted ex vivo, this state responds to polyclonal or Mycobacterium tuberculosis (Mtb) peptide antigen stimulation with interleukin-17 (IL-17) or interferon gamma (IFNg).

  Study phs002467

• Genomics of enteropathy-associated T cell lymphoma (EATL)

  Whole exome sequencing of enteropathy-associated T cell lymphoma (EATL) tumors and paired normals, as well as RNA-sequencing of EATL tumors: including (1) 69 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples, (2) 36 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL paired normal samples, and (3) 32 RNAseq, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples.

  Dataset EGAD00001003284

• Transcriptome sequencing of myelodysplasia

  Transcriptome sequencing was performed on 214 patients with myelodysplasia in this study. RNA was obtained from bone marrow CD34+ cells (n=100) and/or bone marrow mononuclear cells (n=165). Transcriptome sequencing was performed for both cell fractions in 51 patients. A total of 211 patients were genotyped by targeted deep sequencing. We also studied bone marrow CD34+ cells and bone marrow mononuclear cells obtained from three healthy adults each.

  Dataset EGAD00001003891

• Raw sequencing data for donor and patient fecal samples

  Microbiome analysis was performed on the patient samples collected pre-FMT and on days after FMT, and on samples collected from the FMT donor. Genomic bacterial DNA was extracted from fecal samples using the QIAamp DNA Stool kit (Qiagen, Hilden, Germany), with the addition of a bead-beating lysis step. Genomic 16S ribosomal-RNA V4 variable regions were amplified and sequenced on the Illumina MiSeq platform.

  Dataset EGAD00001004371

• RNA sequencing of NK cells in human lung

  The dataset contains RNAseq data from 5 subsets of NK cells isolated from human lung: 1) CD69+CD49a+CD103+CD16-CD56bright NK cells 2) CD69+CD49a+CD103-CD16-CD56bright NK cells 3) CD69+CD49a-CD103-CD16-CD56bright NK cells 4) CD69-CD49a-CD103-CD16-CD56bright NK cells 5) CD56dimCD16+NKG2A+CD57- NK cells The dataset contains paired data for the subsets from 2 donors with 2 biological replicates/donor and subset.

  Dataset EGAD00001004850

• UNITO_Molpheno_Closed

  This dataset contains Whole Genome Sequencing, RNA-sequencing and ATAC-sequencing data obtained from PBMCs derived from blood samples of one patient with complex genomic rearrangements and the biological parents. The patient has multiple congenital anomalies and delayed development. Data access is closed.

  Dataset EGAD00001004863

• Analysis of resistance to PLX4032 (2019-08-21)

  We have collected material from a patient who had BrafV600E mutant melanoma that was treated with PLX4032. We have germline DNA from the patient and DNA and RNA from distinct lesions before and after treatment with PLX4032. We would like to exome sequence these samples to gain a snap shot of the mechanisms of resistance that are operative. . This dataset contains all the data available for this study on 2019-08-21.

  Dataset EGAD00001005278

• 10X 3' V2 data of single immune cells in hepatocellular carcinoma

  The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites. This is the droplet data of this study

  Dataset EGAD00001005961