3659 results for "RNA AND sequencing OR transcriptome"

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• RNA-sequencing of ex vivo exhausted human antigen-specific T cells

  Tumor-specific T cells are frequently exhausted by chronic antigenic stimulation. To explore new pathways for reinvigoration of anti-tumor immune functions, we developed a human ex vivo exhaustion model by repetitive antigenic stimulation of primary CD8 T cells. This results in T cells that resemble patient-derived T cells in tumors on a phenotypic and transcriptional level. Four human healhy donor CD8+ T cells were isolated, transduced with an NY-ESO-1 TCR lentivirus construct, stimulated in four different conditions (Trested, Ttumor, Tex, Teff) with T2 tumor cells and specific peptides over 12 days. Cells were then sorted for TCR Vbeta 13.1+ (NY-ESO-1 TCR) CD8+ CD3+ CD56- CD4- DAPI- cells. RNA-seq TruSeq libraries were generated from polyA-enriched mRNA isolated from the samples, and sequenced in paired-end mode (2x51bp) on 2 lanes of an Illumina NovaSeq 6000 flow-cell. FASTQ sequence files were generated with the Illumina RTA version 3.4.4 and Base-calling Version bcl2fastq-2.20.0.422.

  Dataset EGAD00001009754

• Single cell and plasma RNA sequencing

  Single cell and plasma RNA sequencing for RNA liquid biopsy for hepatocellular carcinoma

  Study EGAS00001005194

• Dataset for NSCLC-RNA

  Rare cancer sequencing data of 45 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008846

• Dataset for liposarcoma-RNA

  Rare cancer sequencing data of 40 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008854

• Single cell and whole tissue transcriptomes investigating Barrett's oesophagus

  Data consists of 4,640 RNA-sequencing sample libraries. These libraries were sequenced from four sites of the upper gastro-intestinal tract (Barrett’s oesophagus, proximal normal oesophagus, proximal normal stomach, and duodenum) in two experiments. 4,587 libraries were produced in the first experiment in which whole transcriptomes were isolated single cells dissociated from endoscopic biopsy tissue obtained from the four previously mentioned tissues. The other 53 libraries were produced in the second experiment in which whole transcriptomes were isolated from whole tissue from endoscopic biopsies of the four previously mentioned tissues. The data found here are stored in the raw fastq file format from paired end sequencing.

  Dataset EGAD00001004344

• RNA-Seq Brest Patient-derived Tumor Organoids

  This dataset includes 14 RNASeq samples from 8 patients. For some patients, organoids at different passages have been profiled. They can be identified by their alias, composed of the following structure: <subjectId>_O<organoid_number>_<passage>_RNA. For example, ICSBCS002_O1_1_RNA indicates the earlier passage of organoid 1 for subject ICSBCS002, and ICSBCS002_O1_2_RNA indicates the later passage. Additionally, WCM2137_O1_RNA and WCM2137_O2_RNA indicate two organoids (O1 and O2) derived from different tissues. More information about the passages and tissues can be found in the sample information table.

  Dataset EGAD50000000960

• De novo modeling of chromoplectic Ewing sarcoma tumors from patient-derived mesenchymal stem cells

  Ewing sarcoma is characterized by pathognomonic translocations fusing most frequently EWSR1 with FLI1 (EF1). In addition, Ewing sarcoma can also display alterations in STAG2, TP53 and CDKN2A (SPC). Starting from Ewing sarcoma derived human mesenchymal stem cells (MSCpat), we recapitulated this translocation and SPC alterations using a CRISPR/cas9 approach and generated a bona fide Ewing sarcoma model (EWIma1) displaying transcriptomic (RNA-seq) and epigenetic (ChIP-seq) hallmarks of EwS.

  Dataset EGAD50000001673

• Whole scRNA-seq from pre frontal cortex patient biopsy

  The single- cell RNA-seq prefrontal cortex sample was selected from a cohort of patients with hydrocephalus ≥18 years of age planning to undergo CSF diversion surgery either with a ventriculoperitoneal shunt placement (VP) or ventriculocisternostomy (VCS). The tissue was dissociated followed by red cell and debris removal and counting of the cells to be sequenced with (scRNA-seq; 10x Genomics kit v2). After dissociation only non neuronal cells were retrieved.

  Dataset EGAD50000001542

• RNAseq from PDAC samples

  BAM files from RNA-seq of PDAC samples used in the COMPASS hENT1 study

  Dataset EGAD00001009409

• Gene expression in CSF and whole blood of adults with proven bacterial meningitis in Malawi

  Dataset of BAM files from patients with proven bacterial meningitis in Malawi. Samples consist of BAM files from PolyA RNA seq runs from patients classifed as admission whole blood or CSF on admission (pre-antibiotics) in the Emergency Department. Subsequent BAM files are identical runs from whole blood from the same patients, taken at either day 10 or day 40 post admission to hospital. All patients have disease, they are divided into survivors and non-survivors at the day 40 time point.

  Dataset EGAD00001004488