7188 results for "({!join from=dataset_studies to=id v=$q1}) OR ("transcriptome" OR "RNA-seq" OR "rna sequencing" OR "rna-sequencing")"

in 69.31 milliseconds.

• Transcriptome sequencing of replication repair deficient brain cancers

  Hypermutant tumors which harbor many somatic mutations may obscure the interpretation of targetable genomic events. This dataset contains transcriptome sequencing from 21 replication repair deficient brain tumor samples as well as healthy controls.

  Dataset EGAD00001006921

• Spatial transcriptome sequence data from prostate cancer needle biopsies

  Spatial transcriptome sequencing data from prostate cancer needle biopsies. Dataset contains biopsies from before and after androgen deprivation therapy of 3 patients with 8 biopsies per patient in total. 2 sections (replicates) are taken from each biopsy.

  Dataset EGAD00001008636

• Nasal Polyp Whole-transcriptome sequencing

  Whole-transcriptome sequencing (RNAseq) in patients with chronic rhinosinusitis with nasal polyps (CRSwNP) and controls. Differential expression patterns in genes involved in cilia, viral defense and NKT-cell specific pathways, suggesting a role of viral immunity in combination with cilia functionality in CRSwNP.

  Dataset EGAD00001010146

• High-throughput transcriptome data of paediatric ETV6-RUNX1 acute lymphoblastic leukemia

  High-throughput transcriptome sequencing data from paediatric (<18-y) ETV6-RUNX1 fusion positive acute lymphoblastic leukemias. Dataset includes fastq and BAM files from diagnostic samples of 33 patients.

  Dataset EGAD00001010164

• WGS and WTS data for manuscript titled: Pathologist-initiated whole genome and transcriptome sequencing demonstrates diagnostic utility in resolving difficult-to-diagnose tumors

  Illumina platform sequencing of whole genome libraries prepared from normal and cancer samples and whole transcriptome libraries from cancer samples from 45 donors

  Dataset EGAD00001015615

• Dataset for whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors for adrenocortical tumors

  Dataset for whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors for adrenocortical tumors

  Dataset EGAD00001000810

• RNAseq files

  Illumina Nextseq 500 whole transcriptome RNAseq from PBMCs - run1

  Dataset EGAD00001006006

• Transcriptome analysis of anaplastic meningiomas

  Transcriptome of anaplastic meingiomas

  Dataset EGAD00001003255

• Transcriptome of (monocytes and dendritic cells ), from donor S8, replicate 1 patient

  Dataset EGAD00001009020

• Transcriptome of (monocytes and dendritic cells ), from donor S6, replicate 1 control

  Dataset EGAD00001009016

• Transcriptome of (monocytes and dendritic cells ), from donor S9, replicate 1 control

  Dataset EGAD00001009022

• Transcriptome of (monocytes and dendritic cells ), from donor S14, replicate 1 control

  Dataset EGAD00001009032

• Transcriptome of (monocytes and dendritic cells ), from donor S9, replicate 2 control

  Dataset EGAD00001009023

• Transcriptome of (monocytes and dendritic cells ), from donor S5, replicate 2 control

  Dataset EGAD00001009015

• Transcriptome of (monocytes and dendritic cells ), from donor S6, replicate 2 control

  Dataset EGAD00001009017

• Transcriptome of (monocytes and dendritic cells ), from donor S14, replicate 2 control

  Dataset EGAD00001009033

• Transcriptome of (monocytes and dendritic cells ), from donor S7, replicate 1 patient

  Dataset EGAD00001009018

• Transcriptome of (monocytes and dendritic cells ), from donor S7, replicate 2 patient

  Dataset EGAD00001009019

• Transcriptome of (monocytes and dendritic cells ), from donor S8, replicate 2 patient

  Dataset EGAD00001009021

• Transcriptome of (monocytes and dendritic cells ), from donor S15, replicate 1 patient

  Dataset EGAD00001009034

• Transcriptome of (monocytes and dendritic cells ), from donor S15, replicate 2 patient

  Dataset EGAD00001009035

• Transcriptome of (monocytes and dendritic cells ), from donor S16, replicate 1 patient

  Dataset EGAD00001009036

• Transcriptome of (monocytes and dendritic cells ), from donor S16, replicate 2 patient

  Dataset EGAD00001009037

• Transcriptome of (monocytes and dendritic cells ), from donor S13, replicate 2 control

  Dataset EGAD00001009031

• Transcriptome of (monocytes and dendritic cells ), from donor S1, replicate 1 control

  Dataset EGAD00001009006

• Transcriptome of (monocytes and dendritic cells ), from donor S1, replicate 2 control

  Dataset EGAD00001009007

• Transcriptome of (monocytes and dendritic cells ), from donor S2, replicate 1 control

  Dataset EGAD00001009008

• Transcriptome of (monocytes and dendritic cells ), from donor S2, replicate 2 control

  Dataset EGAD00001009009

• Transcriptome of (monocytes and dendritic cells ), from donor S3, replicate 1 patient

  Dataset EGAD00001009010

• Transcriptome of (monocytes and dendritic cells ), from donor S3, replicate 2 patient

  Dataset EGAD00001009011

• Transcriptome of (monocytes and dendritic cells ), from donor S4, replicate 1 patient

  Dataset EGAD00001009012

• Transcriptome of (monocytes and dendritic cells ), from donor S4, replicate 2 patient

  Dataset EGAD00001009013

• Transcriptome of (monocytes and dendritic cells ), from donor S5, replicate 1 control

  Dataset EGAD00001009014

• Transcriptome of (monocytes and dendritic cells ), from donor S10, replicate 1 control

  Dataset EGAD00001009024

• Transcriptome of (monocytes and dendritic cells ), from donor S10, replicate 2 control

  Dataset EGAD00001009025

• Transcriptome of (monocytes and dendritic cells ), from donor S11, replicate 1 patient

  Dataset EGAD00001009026

• Transcriptome of (monocytes and dendritic cells ), from donor S11, replicate 2 patient

  Dataset EGAD00001009027

• Transcriptome of (monocytes and dendritic cells ), from donor S12, replicate 1 patient

  Dataset EGAD00001009028

• Transcriptome of (monocytes and dendritic cells ), from donor S12, replicate 2 patient

  Dataset EGAD00001009029

• Transcriptome of (monocytes and dendritic cells ), from donor S13, replicate 1 control

  Dataset EGAD00001009030

• TONIC study RNASeq

  Transcriptome sequencing of 97 matched TNBC breast cancer metastasis samples obtained from 50 unique patients assayed at two timepoints: at baseline (directly after patient randomization), and post-induction treatment or control waiting period. The included raw transcriptome sequencing data (fastq-format) were generated using Illumina HiSeq2500 instruments.

  Dataset EGAD00001004858

• Whole-genome, whole-exome and transcriptome sequencing of pancreatic ductal adenocarcinomas from young adults (NCT MASTER)

  Whole-genome, whole-exome and transcriptome sequencing of pancreatic ductal adenocarcinomas from young adults reveals recurrent NRG1-fusions in KRAS wild-type tumors.

  Dataset EGAD00001004068

• Dataset for Sarcoma RNA sequencing linked from study EGAS00001004813

  Sequencing data of 410 sarcoma tumor runs, which were uploaded to EGAS00001004813. The sequencing was always paired.

  Dataset EGAD00001010276

• RNA Editing Transcriptome

  Transcriptome sequencing data of tumor and 10 matched normal samples of the EGAS00001000495 project

  Dataset EGAD00001000627

• Transcriptome of (peripheral blood), from donor Sample A, replicate 1 Freezing replicates

  Freezing replicates

  Dataset EGAD00001010084

• Transcriptome of (peripheral blood), from donor Sample A, replicate 2 Freezing replicates

  Freezing replicates

  Dataset EGAD00001010085

• Transcriptome of (peripheral blood), from donor Sample A, replicate 1 Technical replicates

  Technical replicates

  Dataset EGAD00001010082

• Transcriptome of (peripheral blood), from donor Sample A, replicate 2 Technical replicates

  Technical replicates

  Dataset EGAD00001010083

• Transcriptome analysis of soft tissue sarcoma

  We characterized mRNA expression profile of soft tissue sarcomas.

  Study EGAS50000001672

• Whole genome and transcriptome sequencing of cancer of unknown primary tumours

  Whole genome and transcriptome sequencing of cancer of unknown primary tumours was used to determine yield of clinical biomarkers for a molecular guided trial or for resolving cancer type of origin. This study includes profiling of germline DNA and tumour DNA and RNA by whole genome and transcriptome sequencing. All samples are in BAM format aligned with GRCh38 reference genome. This dataset includes: 1. Whole genome sequencing (WGS) of 78 cancer of unknown primary tumour samples and 73 matched germline DNA. 2. Whole transcriptome sequencing (WTS) of 69 cancer of unknown primary tumour samples (matched to WGS cases) 3. Whole genome sequencing of 22 cell-free DNA samples from cancer of unknown primary patients and matched Germaine DNA(8 samples matched to tumour WGS)

  Dataset EGAD50000000656

• TARGET-seq+ single-cell transcriptome sequencing

  Single-cell whole transcriptome sequencing data for bone marrow samples from 9 cases with clonal hematopoiesis and 4 control samples. The TARGET-seq+ protocol was used to generate plate-based 3' transcriptome data. For details on cell sorting and the TARGET-seq+ protocol see the methods section of the manuscript. One FASTQ file is provided per cell. Cells are named with their plate and well IDs and the subject ID. Empty wells (no-cell controls) are named "blank". Corresponding genotyping files use the same naming without the "_transcriptome" suffix.

  Dataset EGAD00001011175

• Long read transcriptomes of DM1 patients

  DM1 patient blood transcriptome samples, mix of 6 patients per sample

  Dataset EGAD50000000285

• Improving Transcriptome Fidelity Following Synovial Tissue Disaggregation

  Synovial tissue was collected at the time of arthroplasty from rheumatoid and osteoarthritis arthroplasty. Tissues were left intact or disaggregated with different methods to evaluate the effect on the transcriptome.

  Study phs002991

• Transcriptome atlas of brain organoid developent

  Single-cell Cut&Tag of three histone modifications and chromatin accessibility over a timecourse of brain organoid development from pluripotency. We profiled 5 time points of brain organoid development and 2 time points of retinal organoid development. We used scRNA-seq to profile transcriptome. Library preparation was carried out with the 10x genomics platform.

  Dataset EGAD50000000223

• Dataset for single cell transcriptome sequencing

  This datasets contains single cell transcriptome sequencing of 10 control samples. Sequencing has been performed on Illumina NovaSeq 6000 using 10xGenomics Chromium Next GEM Single Cell 5 Reagent Kits. Sequencing was always paired. This dataset additionally contains a .QS file from Seurat Analysis performed in R, generated as described in the related publication.

  Dataset EGAD50000001549

• Whole transcriptome sequencing of C1498 cells.

  The dataset contains raw data (FASTQ) of whole transcriptome sequencing of C1498 cells (n=1 sample). Libraries were prepared with the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina, San Diego, CA, USA) and and 100bp paired-end reads were generated on the NovaSeq 6000 Sequencing System (Illumina).

  Dataset EGAD50000002404

• Single-cell transcriptome of human fetal pancreas and in vitro pancreatic spheroids

  This dataset combines single cell transcriptome data from fetal pancreas at 7-10 wpc, embryonic stem cell-derived pancreas progenitors and spheroids generated from both fetal pancreas and human pluripotent stem cell-derived pancreas progenitors.

  Dataset EGAD00001007506

• Transcriptome dataset from: Biased allelic expression in human primary fibroblast single cells.

  Dataset EGAD00001001084

• Poly A transcriptom sequencing of mutifocal hepatocellular carcinoma

  Poly A transcriptome sequence of mutifocal hepatocelular carcinoma

  Dataset EGAD00001003231

• Transcriptome of (peripheral blood), from donor Sample A, replicate 1 FACS processing technical replicates

  FACS processing technical replicates

  Dataset EGAD00001010086

• Transcriptome of (peripheral blood), from donor Sample A, replicate 2 FACS processing technical replicates

  FACS processing technical replicates

  Dataset EGAD00001010087

• RCRF release 1

  Transcriptome sequencing from the Rare Cancer Research Foundation: leiomyosarcoma, large cell neuroendocrine carcinoma, clear cell carcinoma

  Dataset EGAD00001010198

• Fibromyalgia versus small fiber neuropathy: Diverse keratinocyte transcriptome signature

  We provide a diverse keratinocyte transcriptome signature between SFN and FMS patients, which may hint towards distinct pathomechanisms of small fiber sensitization and lay the basis for advanced diagnostics in both entities

  Study EGAS00001005004

• Transcriptome/Exome for glioblastoma intra-tumoral heterogeneity

  Total of 49 tumor specimens from 20 patients were subjected for whole-exome and/or whole-transcriptome sequencing including matched normal/blood. Tumor samples are acquired based on 4 categories; 1) locally adjacent tumors, 2) multifocal/multicentric tumors, 3) 5-ALA (+/-) tumors and 4) Longitudinal tumors.

  Dataset EGAD00001002248

• Transcriptome and Exome from longitudinal samples of human glioblastoma (newly added after 2015)

  We expanded our previous collection of longitudinal GBM patients (EGAS00001001041) by recruiting 21 additional patients. Tumor specimens were subjected to whole-exome sequencing (16 of 21 cases, with the matched normal/blood) and transcriptome sequencing (16 of 21 cases).

  Dataset EGAD00001002143

• PacBio long-read scRNA-seq

  Full-length single-cell cDNA PacBio Kinnex whole-transcriptome sequencing data for adrenal sampleA and sampleB.

  Dataset EGAD50000002211

• RNA-Seq of human longitudinal whole blood samples from PCR-positive and PCR-negative recent household contacts of COVID-19 index cases.

  Little is known about the transcriptomic profile of individuals who are exposed to SARS-CoV-2 yet resist becoming PCR positive. To investigate this, longitudinal whole-blood samples were taken (0, 7, 14, and 28 days after enrolment) from PCR positive and PCR negative SARS-CoV-2-naïve household contacts who were recently exposed to a COVID-19 index. Samples were also taken from pre- and post-pandemic unexposed controls. Total RNA was extracted from PAXgene tubes before undergoing poly(A) selection followed by 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 across 2 flowcells of an Illumina HiSeq 4000.

  Study EGAS50000000473

• RNA-seq of Glioblastoma stem cells

  Chromatin accessibility discriminates stem from mature cell populations, enabling the identification of primitive stem-like cells in primary tumors, such as Glioblastoma (GBM) where self-renewing cells driving cancer progression and recurrence are prime targets for therapeutic intervention. We show, using single-cell chromatin accessibility, that primary GBMs harbor a heterogeneous self-renewing population whose diversity is captured in patient-derived glioblastoma stem cells (GSCs). In depth characterization of chromatin accessibility in GSCs identifies three GSC states: Reactive, Constructive, and Invasive, each governed by uniquely essential transcription factors and present within GBMs in varying proportions. Orthotopic xenografts reveal that GSC states associate with survival, and identify an invasive GSC signature predictive of low patient survival. Our chromatin-driven characterization of GSC states improves prognostic precision and identifies dependencies to guide combination therapies.

  Study EGAS00001003070

• Influence of the Microbiome on Epigenetic Mechanisms in IBD

  Live CD4 T cells were sorted from inflamed and non-inflamed tissue samples of IBD patients or from healthy and IBD blood samples. ATAC-Seq libraries were generated from live CD4 T cells sorted from i) inflamed and non-inflamed tissue samples, ii) healthy and IBD blood samples, or from iii) CD4 T cell subsets polarised from healthy blood samples. After isolating crude nuclei, live CD4+ T cells were treated with Tagment DNA buffer and Tagment DNA Enzyme (Nextera DNA Library Prep Kit, Illumina), and then the DNA was purified by MinElute PCR Purification Kit (Qiagen). Transposed DNA fragments were amplified using specific adapters followed by purification with MinElute PCR Purification Kit (Qiagen). Fragments from 240-360pb were selected in the PippinHT system (Sage Science). The quality of the library and its DNA concentration were assessed by Bioanalyzer instruments (Agilent Technologies) and ultimately submitted for sequencing using Illumina HiSeq 2500 sequencer, V4 chemistry. On the other hand, single cell RNA-Seq libraries were generated exclusively from inflamed and non-inflamed tissue samples of Crohn’s disease patients. Briefly, live CD4 T cells were captured and encapsulated before cDNA amplification using the 10X Genomics Chromium Platform. Samples were prepared as outlined by 10x genomics Single Cell 3’ Reagent Kits v2 user guide. Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1 – 26 cycles, read 2 – 98 cycles, index 1 – 8 cycles.

  Dataset EGAD00001011066

• FOXM1 is a biomarker of resistance to PI3Kα inhibition in ER+ breast cancer that is detectable using metabolic imaging (RNA-seq data)

  PIK3CA, encoding the PI3Kα isoform, is the most frequently mutated oncogene in estrogen receptor-positive breast cancer. Isoform-selective PI3K inhibitors are used clinically but intrinsic and acquired resistance limits their utility. Improved selection of patients that will benefit from these drugs requires novel predictive biomarkers. We show here that persistent FOXM1 expression following drug treatment is a biomarker of resistance to PI3Kα inhibition in ER+ breast cancer. Since the transcription factor drives expression of lactate dehydrogenase (LDH) but not hexokinase 2 (HK-II), changes in FOXM1 expression can be detected using magnetic resonance imaging of LDH-catalyzed hyperpolarized 13C label exchange between pyruvate and lactate but not by PET measurements of HK-II-mediated trapping of the glucose analog 2-deoxy-2-[18F]fluorodeoxyglucose.

  Study EGAS00001004452

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells - untreated) from donor D1, replicate 2, glucose concentration 5mM

  Dataset EGAD00001008038

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells - untreated) from donor D3, replicate 1, glucose concentration 5mM

  Dataset EGAD00001008057

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells - untreated) from donor D1, replicate 1, glucose concentration 5mM

  Dataset EGAD00001008037

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells - untreated) from donor D2, replicate 1, glucose concentration 5mM

  Dataset EGAD00001008047

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells - untreated) from donor D2, replicate 2, glucose concentration 5mM

  Dataset EGAD00001008048

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells - untreated) from donor D3, replicate 2, glucose concentration 5mM

  Dataset EGAD00001008058

• Childhood_arthritis_DNA

  The aim of this study is to describe the transcriptome of single arthritic cells.

  Study EGAS00001002652

• Whole-genome and transcriptome sequencing data of an undifferentiated gastric spindle cell sarcoma

  Dataset EGAD00001006014

• GBM-Space: Joint Transcriptome and Chromatin Accessibility Profiling of Glioblastoma (10x Genomics - Multiome)

  GBM-Space: Joint Transcriptome and Chromatin Accessibility Profiling of Glioblastoma (10x Genomics - Multiome)

  Dataset EGAD00001015526

• Whole-transcriptome characterization of cell-free RNA (cfRNA) in cancer and non-cancer patients

  Whole-transcriptome characterization of cfRNA in cancer (stage III breast [n=46], lung [n=30]) and non-cancer (n=89) participants from the Circulating Cell-free Genome Atlas (NCT02889978). Dataset includes collapsed BAM files for plasma cfRNA from each patient, as well as collapsed BAM files for RNA from matched tumor tissue (when available).

  Dataset EGAD00001006484

• Genome and transcriptome sequencing of cancer of unknown primary tumours

  Genome and transcriptome sequencing of cancer of unknown primary tumours was used to determine yield of clinical biomarkers for a molecular guided trial or for resolving cancer type of origin. This study includes profiling of germline DNA and tumour DNA by whole genome sequencing of tissue and cfDNA biopsies, as well as targeted genome sequencing using two panels, including Comprehensive cancer panel (CCP) and TruSight Oncology 500 (TSO500). This study also includes profiling of tumour RNA by whole transcriptome sequencing.

  Study EGAS50000000452

• Whole-genome and transcriptome sequencing of a patient with extrapancreatic acinar cell carcinoma

  Dataset EGAD00001006023

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Rotenone from donor D3, replicate 2, glucose concentration 5mM

  Dataset EGAD00001008062

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Resveratrol from donor D3, replicate 1, glucose concentration 5mM

  Dataset EGAD00001008059

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Oligomycin from donor D2, replicate 2, glucose concentration 5mM

  Dataset EGAD00001008054

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Oligomycin from donor D2, replicate 1, glucose concentration 1mM

  Dataset EGAD00001008055

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Oligomycin from donor D2, replicate 2, glucose concentration 1mM

  Dataset EGAD00001008056

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Resveratrol from donor D3, replicate 2, glucose concentration 5mM

  Dataset EGAD00001008060

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Rotenone from donor D3, replicate 1, glucose concentration 5mM

  Dataset EGAD00001008061

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Oligomycin from donor D3, replicate 1, glucose concentration 5mM

  Dataset EGAD00001008063

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Oligomycin from donor D3, replicate 2, glucose concentration 5mM

  Dataset EGAD00001008064

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Oligomycin from donor D3, replicate 1, glucose concentration 1mM

  Dataset EGAD00001008065

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Oligomycin from donor D3, replicate 2, glucose concentration 1mM

  Dataset EGAD00001008066

• Transcriptome of human CD4+ T-lymphyocyte (naive-T-cells) treated with Resveratrol from donor D1, replicate 1, glucose concentration 5mM

  Dataset EGAD00001008067

• Transcriptome of human CD4+ T-lymphyocyte (naive-T-cells) treated with Resveratrol from donor D1, replicate 2, glucose concentration 5mM

  Dataset EGAD00001008068

• Transcriptome of human CD4+ T-lymphyocyte (regulatory-T-cells) treated with Resveratrol from donor D1, replicate 1, glucose concentration 5mM

  Dataset EGAD00001008069

• Transcriptome of human CD4+ T-lymphyocyte (regulatory-T-cells) treated with Resveratrol from donor D1, replicate 2, glucose concentration 5mM

  Dataset EGAD00001008070

• Transcriptome of human CD4+ T-lymphyocyte (naive-T-cells) treated with Resveratrol from donor D2, replicate 1, glucose concentration 5mM

  Dataset EGAD00001008071

• Transcriptome of human CD4+ T-lymphyocyte (naive-T-cells) treated with Resveratrol from donor D2, replicate 2, glucose concentration 5mM

  Dataset EGAD00001008072

• Transcriptome of human CD4+ T-lymphyocyte (memory-T-cells) treated with Resveratrol from donor D1, replicate 1, glucose concentration 5mM

  Dataset EGAD00001008039