3928 results for "RNA AND sequencing OR transcriptome"

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• Analysis of chromosomal background of cancerous mutations using a long-read sequencer

  In our previous study detecting cancerous complex SVs, we performed whole-genome sequencing of lung cancer clinical samples using PromethION. In this study, its depth and quality was substantially enriched and we conducted the phasing analysis in human lung cancer genomes. In addition, long read and short read RNA-seq was performed for transcriptome analysis.

  Study JGAS000349

• SARS-CoV-2 induced alterations of the upper airway DNA methylome exert long-term impacts on ciliary genes involved in ciliary function

  Enzymatic DNA methylome (n=33) and single-cell RNA (n=24) sequencing were performed in nasal cells of COVID-19 patients and controls. In addition, we re-sampled a subset of patients for transcriptome analyses at 3 and 12 months post-infection and followed the expression of differentially regulated genes over time.

  Study EGAS50000000273

• RNA-Seq data of hepatoma (Huh7 derived) and Ph5CH cells and primary hepatocytes

  The innate immune response of cells of hepatic origin (Huh7, Huh7.5, PH5CH and primary human hepatocytes (PHH), 66 samples) was analyzed by transcriptome analysis (RNAseq) upon supernatant delivery or transfection of synthetic dsRNA (poly(I:C)). Expression of TLR3 and RIG-I was reconstituted by lentiviral transduction in Huh7 and Huh7.5 cells. The sequencing is single RNA-Seq on an Illumina HiSeq 4000 with the Illumina TruSeq stranded mRNA kit.

  Dataset EGAD00001007083

• Genomic characterization of aggressiveness in pituitary neuroendocrine tumors (PitNETs)

  RNA sequencing data of 227 samples of PitNETs in the context of the genomic characterization of aggressiveness of PitNETs

  Dataset EGAD50000002050

• HIPO blastemal Wilms (nephroblastoma) RNA sequencing samples

  HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving gene expression events

  Dataset EGAD00001000993

• bladder cancer patient data

  This contains H3K27ac ChIP-seq, RNA-seq and HiC fastq files.

  Dataset EGAD00001007052

• Single-cell RNA-sequencing of H3-K27M diffuse midline glioma.

  Fastq files are deposited for single-cell transcriptomes of patient H3-K27M diffuse midline gliomas, generated using the SMART-seq2 method.

  Dataset EGAD00001011339

• RNA sequencing of undifferentiated sarcomas

  mRNA sequencing of 50 undifferentiated sarcoma tumour samples and 5 adjacent muscle tissue samples. BAM files are provided, with metadata specifying which samples are tumour/normal.

  Dataset EGAD00001004439

• Single cell sequencing in CNS autoimmune disease

  RNA, T cell receptor and B cell receptor single cell sequencing data generated on T and B cells derived from patients with CNS autoimmune disease

  Dataset EGAD00001006232

• Single-cell mRNA-sequencing of neuroblastoma

  Profiling of childhood neuroblastoma by single-cell RNA sequencing

  Dataset EGAD00001009766

• Sequencing of uveal melanoma metastases

  Whole genome, exome and RNA sequencing of uveal melanoma metastases, primary tumors and matched normal DNA.

  Dataset EGAD00001006031

• Bulk RNASeq of metastatic colorectal cancer organoids with ATOH1 knockout

  Bulk RNA sequencing was performed on mCRC organoids subjected to cetuximab treatment, comparing ATOH1 knockout and control conditions. The dataset is intended to elucidate the contribution of ATOH1-regulated secretory cell population to cetuximab persistence mechanisms.

  Study EGAS50000001421

• single cell data from HPV-positive head and neck cancer patients receiving induction CTLA-4 and PD-1 immune checkpoint blockade

  Baseline and on-treatment tumor samples from human papillomavirus-positive oropharynx cancer patients receiving anti-CTLA-4 and anti-PD-1 immune checkpoint blockade were analyzed by single-cell RNA and TCR sequencing.

  Study EGAS50000000335

• RNA-Sequencing data of Fusobacterium nucleatum treated CAFs and HT-29 tumor spheroid exposed to Fusobacterium nucleatum treated CAFs conditioned medium.

  RNA-Sequencing data of CAFs (patient derived CAF180 and CAF181 as well as the CT5.3 CAF cell line) and HT-29 tumor spheroid samples performed in the context of the study of the interaction of Fusobacterium nucleatum with CRC CAFs. Fusobacterium nucleatum interacts with cancer-associated fibroblasts to enhance colorectal cancer progression

  Dataset EGAD50000001614

• B cells (CD19) RNAseq dataset of JIA patients with known uveitis status.

  CLUSTER consortium RNA sequencing dataset from UK JIA patient cohort with documented uveitis status. Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples and cryopreserved. Samples were subsequently thawed and flow-sorted for CD19+ B cells prior to RNA sequencing. Clinical metadata includes patient demographics and uveitis status at time of sampling.

  Dataset EGAD50000001616

• SCIMAP PILOT D21

  This dataset includes the RNA-seq and ATAC-seq fastq files, as well as the Cellranger ARC count table, for the first experiment with multimodal sequencing in the SCI-MAP project (1 sample). Here, human induced pluripotent stem cells underwent differentiation to chondrocytes for 21 days following an established protocol. Nuclei were isolated and sequenced in two modalities simultaneously; RNA and ATAC.

  Dataset EGAD50000001516

• Transcriptomic dataset from a phase II study of pembrolizumab and epigenetic modification with azacitidine in platinum-resistant epithelial ovarian cancer

  This dataset includes sequence files from bulk RNA sequencing of tissue biospecimens from a phase II study investigating epigenetic priming followed by immune checkpoint blockade in platinum-resistant epithelial ovarian cancer (NCT02900560). There are 48 bulk RNA sequencing files from 24 specimens included in this dataset.

  Dataset EGAD50000001664

• Transcriptomic and chromatin accessibility profiling in T cells for the MTOR genetics paper.

  This submission contains raw ATAC and RNA sequencing data from human primary CD4+ and CD8+ T cells, either stimulated or unstimulated with anti-CD3/CD28 Dynabeads, from three healthy donors. It includes 24 paired-end FASTQ files consisting of 12 poly(A)-enriched RNA-seq samples and 12 ATAC-seq samples sequenced on the Illumina NextSeq 500 platform.

  Dataset EGAD50000001307

• Single-cell RNA-sequencing of CSF cells and PBMCs from individuals with neurological disorders

  We undertook single-cell RNA sequencing to establish gene expression and lymphocyte receptor sequences of CSF and peripheral blood leukocytes derived from patients with a variety of inflammatory, infectious and non-inflammatory neurological disorders. The aim of the study was the investigation of functional changes of the cells involved in neuroinflammatory responses.

  Dataset EGAD50000001173

• TIRE-seq_PDN

  TIRE-seq is a novel RNA sequencing method that integrates mRNA purification directly into library preparation, eliminating separate RNA extraction. The technique demonstrated utility across three biological applications, including capturing transcriptional changes in human T cells, identifying genes driving murine dendritic cell differentiation, and analyzing the dose-response effects of temozolomide on patient-derived neurospheres. With its simplified approach and high sequencing efficiency, TIRE-seq offers a cost-effective solution for large-scale gene expression studies.

  Dataset EGAD50000001261

• oncogenic gene fusions in primary colon cancers

  This dataset represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. RNA-sequencing was performed using TruSeq library preparation and samples were sequenced on Illumina NextSeq and HiSeq. The data are available as Illumina NextSeq and HiSeq fastq files (_R1.fastq and _R2.fastq for each tumor sample, 556 files in total).

  Dataset EGAD00001003291

• RNA-sequencing of six Pilocytic astrocytoma tumors

  Total stranded TruSeq RNA sequencing by Illumina of six tumor samples from six cases of pediatric Pilocytic astrocytoma. The data is published in the following paper: Tomic TT, Olausson J, Wilzen A, Sabel M, Truve K, Sjogren H, Dosa S, Tisell M, Lannering B, Enlund F, Martinsson T, Aman P, Abel F. A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma. PLoS One. 2017 Apr 27;12(4):e0175638.

  Dataset EGAD00001003143

• Evolution of four ER+ breast cancers

  The evolution of four breast cancers was analyzed using longitudinal samples collected over 2-15 years. Whole-genome sequencing and single-cell RNA-Seq were used to analyze evolution. We have deposited VCF files for SNV, indel, and structural variant calls from WGS data, and a text file showing transcripts per million (TPM) expression for the single-cell RNA-Seq data.

  Dataset EGAD00001003303

• Data for Paper: Combining transcription factor binding affinities with open chromatin data for accurate gene expression prediction

  mRNA, total RNA, small noncoding RNA, NOMe-Seq and DNase-Seq data from following samples (not every Sequencing Type for every sample): 01_HepG2_LiHG_Ct1 41_Hf01_LiHe_Ct 41_Hf02_LiHe_Ct 41_Hf03_LiHe_Ct 51_Hf03_BlCM_Ct 51_Hf04_BlCM_Ct 51_Hf03_BlEM_Ct 51_Hf04_BlEM_Ct 51_Hf03_BlTN_Ct 51_Hf04_BlTN_Ct Metadata available at deep.dkfz.de

  Dataset EGAD00001002735

• Single cell RNA sequencing of colorectal cancer

  To understand intrinsic cancer cell signatures and the surrounding microenvironemt and their interactions, we performed single-cell RNA sequencing on 63,689 cells from 23 patients with 23 primary colorectal cancer and 10 matched normal mucosa samples. Analyzing of primary colorectal cancer and normal mucosa samples show a comprehensive cellular landscape of colon cancer, which is a valuable resource for the development of therapeutic strategies.

  Dataset EGAD00001005198