14995 results for "cancer studies using rna-seq"

in 13.41 milliseconds.

• Transcriptome - Uveal Melanomas

  Total RNA sequencing on 9 uveal melanomas. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599). Paired-end libraries (2 x 100 bp) were sequenced on a NovaSeq 6000 instrument (Illumina).

  Dataset EGAD50000000763

• Single cell RNA-sequencing of glioblastoma tumours

  Single cell RNA-sequencing of fresh glioblastoma tumor biopsies with 10x Genomics 3' expression (v2 chemistry). Aligned to GRCh38 reference genome using CellRanger.

  Dataset EGAD00001006803

• Transcriptome analysis of human longitudinal whole blood samples from PCR-positive and PCR-negative adults following controlled inoculation with Influenza A (H3N2) virus.

  Transcriptome analysis of influenza A (H3N2) human challenge samples. Understanding of the transcriptomic profile of individuals in early influenza infection is limited. To investigate this, longitudinal whole-blood samples (n=178) were taken from adult participants following controlled inoculation with Influenza A H3N2 virus (sampling at baseline (0) and days 1, 2, 3, 7, 10 and 14 post-challenge). Most participants became influenza PCR-positive; a minority remained PCR-negative. Total RNA was extracted from PAXgene tubes before undergoing globin and rRNA depletion. DNA libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. All samples were then sequenced using Illumina NovaSeq 6000.

  Study EGAS50000000679

• Single-cell RNA sequencing analysis of corneal and limbal epithelial cells derived from a patient with congenital aniridia

  Aniridia-associated keratopathy (AAK) is a progressive condition characterized by conjunctivalization of the cornea, yet its molecular mechanisms remain largely unknown. This study aims to elucidate the transcriptional landscape of AAK by characterizing the gene expression profiles of corneal epithelial cells in a patient with congenital aniridia. Corneal and limbal epithelial tissues were collected from the patient during the cultivated oral mucosal epithelial transplantation (COMET) surgery. The tissues were dissociated into single cells and subjected to single-cell RNA-seq.

  Study JGAS000790

• RNA-seq data from 9 patients with peri-implantitis

  Fastq files + patients' characteristics

  Dataset EGAD50000000544

• RNA-seq of murine osteosarcoma cell line genetically modified for CYR61

  Transcriptomic analysis of K7M2 murine osteosarcoma cells stably modified to overexpress or repress CYR61

  Dataset EGAD50000000747

• RNA-Seq of SMARCB1 re-expression and HDAC+mTOR inhibition experiments in malignant rhabdoid tumor organoids

  Dataset EGAD00001006574

• RNASEQ_TALL_t_14_16_translocation

  RNA-seq results of sequenced data of patients with t(14;16) translocated T-ALL.

  Dataset EGAD50000001781

• Transcriptomic 90 patient cohort data

  This dataset includes RNA-seq data of samples from our paper.

  Dataset EGAD00001009042

• MSAT dataset

  Muscle SATellite cell study (MSAT) dataset comprises 39 samples of paired-end RNA-Seq sequences in fastq format.

  Dataset EGAD00001008984

• Biomarker data

  Biomarker data for KATHERINE: Biomarker data include RNA-seq time point, Percent of tumor content, PAM50 subtypes, normalized gene expression of ERBB2, CD8 and CD274, normalized immune signature expression.

  Dataset EGAD00001008786

• Spatial Transcriptomics of Vaccine Therapy With or Without Cyclophosphamide in Treating Patients Undergoing Chemotherapy and Radiation Therapy for Stage I or Stage II Pancreatic Cancer That Can Be Removed by Surgery

  Pancreatic ductal adenocarcinoma (PDAC) is a rapidly progressing cancer that responds poorly to immunotherapies. Intratumoral tertiary lymphoid structures (TLS) have been associated with rare long-term PDAC survivors, but the role of TLS in PDAC and their spatial relationships within the context of the broader tumor microenvironment remain unknown. Here, spatial transcriptomics data were generated from 16 pancreatic cancer patients treated with GVAX, whose tumors presented with induced intratumoral TLS. Resected tumor specimens were embedded in OCT media and freshly frozen. Sections were cut into 6.5 x 6.5 mm dimensions compatible with Visium spatial transcriptomics slides. TLS-positive tumor sections from 14 patients (14 tumor samples in total) and lymph nodes from remaining patients (2 lymph node samples in total) were selected by an expert pathologist for profiling. We used 4 Visium slides and covered the 16 capture areas with sections cut in a cryostat at 10 µm. The fresh frozen Visium protocol was followed according to manufacturer's recommendations (10x Genomics Spatial 3' v1). Tissue permeabilization and library construction was carried out according to the manufacturer's protocols. Permeabilization time was optimized to 30 minutes. The captured tissue sections were permeabilized to allow RNA to be captured onto the slide where it reverse-transcribed to cDNA. The cDNA was then amplified, and sequencing libraries were prepared using the 10x Genomics Visium Spatial Gene Expression Reagent Kit for Library Preparation. The libraries were then sequenced using an Illumina NovaSeq sequencer. The raw data obtained from the sequencing were processed using the SpaceRanger (spaceranger-1.2.0) pipeline for alignment onto the GRCh38-2020-A reference transcriptome quantification of gene expression. Unsupervised learning generated a TLS-specific spatial gene expression signature that significantly associates with improved survival in PDAC patients. These analyses demonstrate TLS-associated intratumoral B cell maturation.

  Study phs003862

• MIBC NAC2020 cohort RNA sequencing

  The dataset contains RNA sequencing data from N=48 transurethral resections of bladder tumours (TURBTs) from N=48 patients with muscle-invasive bladder cancer. All TURBTs originate from formalin-fixed paraffin embedded tissue. We used the Illumina TruSeq RNA exome kit, previously known as the TruSeq RNA Access Library Prep Kit. This kit converts total RNA into template molecules of known strand origin, followed by sequence-specific capture of coding RNA. All samples were run in an Illumina NovaSeq6000 instrument. Paired FASTQ files from all 48 patients are provided.

  Study EGAS50000000741

• Sequencing data for oesophageal and related samples - Xiaodun Li et al (WGS, RNA)

  Data supporting: "Esophageal adenocarcinoma organoid cultures recapitulate human disease heterogeneity and provide a model for clonality studies and precision therapeutics." Li et al. WGS (BAM files) RNAseq (BAM files) Tumours, organoids, normals

  Dataset EGAD00001004007