12214 results for "cancer rna-seq"

in 35.55 milliseconds.

• ChIP-seq on Hodgkin lymphoma DAC

  Dac EGAC00001001007

• Henssen Lab Neuroblastoma Circle-seq Data

  Dac EGAC00001001803

• Henssen Lab Neuroblastoma Circle-seq Data

  Dac EGAC00001001804

• Human Inflammatory Skin Disease scRNA-seq

  Dac EGAC00001002309

• RNA sequencing data of pediatric B-other acute lymphoblastic leukemia

  For a long time, approximately 70% of childhood B-ALL cases could be classified routinely, and the remaining 30% were classified into the “B-other” group lacking the known genetic features. However, more recently, new genomic tools have uncovered new subtypes among the B-other groups. Approximately 10% of B-ALL cases lack the recurrent genetic abnormalities, and are referred as "B-other". They are typically more heterogeneous than other subtypes of B-ALL, and their prognoses are more variable. In a more recent update of the B-ALL classification, 27 subtypes were identified (Arber et al., 2022). The identification of some of these subtypes is dependent on NGS methods, such as RNA sequencing, which are not routinely used in all clinical laboratories. For example, ETV6::RUNX1-like and DUX4-rearranged subtypes have been identified using RNA sequencing. For this study, subtype predictions for some of the cases were acquired by using the ALLIUM (Krali et al., NPJ Precis Oncol., 2023) and ALLCatchR (Beder et al., Blood, 2022) tools for the RNA sequencing data.

  Study EGAS50000001803

• Epigenetic analysis of clear cell renal cell carcinoma using ChIP-seq

  To investigate the epigenetic landscape of clear cell renal cell carcinoma (ccRCC), we performed ChIP-seq data for the CTCF, H3K4me1, H3K4me3, H3K27ac, H3K27me3, H3K36me3, and HIF1A marks in the 786-O, A-498, UM-RC-2 ccRCC cell lines, as well as the HK-2 normal renal epithelium cell line, cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. Data are provided in raw fastq and narrowPeak formats. Data were processed using the nf-core chipseq pipeline.

  Dataset EGAD50000001886

• 5 scRNA-seq with TCR Enrichment of Tumour-Involved Lymph Nodes, Malignant Seromas and Patient-Derived Xenografts from 18 T-Cell Lymphoma Patients

  This raw data contains 5' scRNA-seq with TCR enrichment data from 18 individual patients analysing cells taken from tumour-involved lymph nodes (LN), malignant seromas and patient-derived xenografts (PDX) including systemic/nodal ALK+ ALCL (n=3 PDX), BIA-ALCL (n=2 seromas), PTCL-NOS (n=5 nodal tumours), nodal T follicular helper lymphoma - angioimmunoblastic type (nTFHL-AI) (n=1), nTFHL, not otherwise specified (nTFHL, NOS, n=1), TLBL (n=5) and 1 case of Sezary Syndrome (SS, cutaneous tumour). Droplet-based 5’ scRNA-seq with TCR enrichment (10x Chromium platform) was performed for all live cells, or the viable CD45+CD3- and CD45+CD3+ fractions following cell sorting by flow cytometry.

  Dataset EGAD00001015703

• Whole Exome and RNA Sequencing of 22 Patient-Derived Xenografts from Estrogen Receptor-Positive Breast Cancers

  We performed RNA and whole exome sequencing on 22 patient-derived xenografts (PDX) from estrogen receptor-positive (ER+) breast cancers, in the presence and absence of estradiol (E2) supplementation. Exome coverage across more than 3,500 clinically relevant genes that previously were covered below 20X (~2.72Mb) was achieved. On average, 11.2Gb of unique sequence data were generated with 95.3% of the bases in the exome design covered to 20x read depth or greater. RNA sequencing was generated from xenograft tumors. Between 50 and 85M total reads were performed. The average strand-specificity and rRNA rate was 98% and 1.5%, respectively. Transcripts for 17,000 to 27,087 genes were detected in these samples.

  Study phs003324

• Tumor reactive γδ T cells contribute to a complete response to PD-1 blockade in a Merkel cell carcinoma patient

  Single cell RNA and TCR sequencing of gamma delta T cells from two Merkel cell carcinoma patients

  Study EGAS50000000102

• Brain tumor sequencing data

  This study contains tumor DNA (with matched normal) for 1 medulloblastoma and 1 ependymoma patient. Tumor RNA sequencing data is also present for the medulloblastoma patient

  Study EGAS00001006352

• RNA Dataset

  The RNA dataset includes 5 samples analyzed with the Oncomine Comprehensive Assay (OCA) panel. After library preparation, sequencing was performed on the Ion Torrent S5 System, generating FASTQ files. The analysis captures gene fusions and splice variants relevant to oncogenic processes. (idem)

  Dataset EGAD50000002502

• RNA isoform diversity, splicing variants, and switching in single cells of the Alzheimer’s disease brain

  Paired 10X 3' single-nucleus RNA sequencing with PacBio Kinnex long-read sequencing in 7 control and 8 Alzheimer's disease human frontal cortex samples.

  Dataset EGAD50000002124

• RNA-Sequencing of whole blood collected from RNU4ATAC/RNU6ATC patients and controls

  RNA-Sequencing of whole blood collected from patients with biallelic RNU4ATAC/RNU6ATAC variants, parents who carry the variants, healthy controls and type 1 diabetes controls.

  Dataset EGAD50000002242

• fibroblast transcriptome of pediatric patients with epilepsy

  RNA sequencing of fibroblasts from pediatric patients with childhood epilepsy. Fibroblast RNA was extracted at passage 3-6 using MN nucleospin, >90M 150bp paired-end reads per sample were obtained with illumina sequencing. Reads were aligned to hg38.

  Dataset EGAD50000001166

• DNA sequencing of sgRNAs in CRISPR-Cas9 screening and RNA sequencing of SF3B4-overexpressing liver organoids

  DNA sequencing of sgRNAs in CRISPR-Cas9 screening and RNA sequencing of SF3B4-overexpressing liver organoids

  Dataset EGAD50000001240

• RNA sequencing of pediatric BCP ALL

  RNA sequencing data of 33 B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) cases were constructed on an Illumina nextseq 2000 Sequencing System.

  Dataset EGAD50000001125

• Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols

  This dataset contains single-cell RNA sequencing and time-course bulk RNA sequencing data of brain organoids grown from multiple cell lines using four different protocols recapitulating dorsal and ventral forebrain, midbrain, and striatum.

  Dataset EGAD50000000938

• RNA sequencing of OM-ALI cultures derived from control and AD individuals exposed to SARS-CoV-2

  RNA sequencing of air-liquid interface (ALI) cultures of olfactory mucosa (OM) cells derived from control (n=3) and AD (n=3) individuals exposed to SARS-CoV-2.

  Dataset EGAD50000000598

• Single-cell RNA and TCR-sequencing of treatment-refractive immune-mediated arthritis

  Single-cell RNA and TCR-sequencing of three patients with treatment-refractive immune-mediated arthritis. The dataset consists of synovial tissue CD4+ and CD8+ T cells and peripheral blood CD45+ leukocytes.

  Dataset EGAD50000000749

• HERBY trial RNASeq

  RNA sequencing of non-brainstem paediatric high grade glioma from the HERBY phase II randomised trial. RNA from fresh frozen surgical tissue in 20 cases was subjected to Illumina whole transcriptome paired end sequencing. Data is provided as paired-end FASTQ files

  Dataset EGAD00001004070

• RNA bam files of Renal Cell Carcinoma patients

  the dataset contains RNA bam files of Renal Cell Carcinoma patients, which belongs to "An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors"

  Dataset EGAD00001003895

• RNA sequencing data of Atypical teratoid/rhabdoid tumors (ATRT)

  RNA sequencing data of Atypical teratoid/rhabdoid tumors (ATRT)

  Dataset EGAD00001002136

• EGAS00001003405 combined RNA, WES, WGS data of 16 gastrointestinal tumor patients

  50 samples of 16 individuals with Gastrointestinal Tumor. Patients were sequenced in various combinations of WGS, Exome and RNA sequencing.

  Dataset EGAD00001005113

• TST170 Pilot RNA VCF

  TST170 Pilot RNA VCF

  Dataset EGAD00001005710

• TST170 Pilot RNA FASTQ

  TST170 Pilot RNA FASTQ

  Dataset EGAD00001005711

• Single-cell RNA sequencing of bronchoalveolar lavages from COVID-19 patients

  Single-cell RNA sequencing of bronchoalveolar lavages from COVID-19 patients.

  Dataset EGAD00001006893

• RNA data of neuroblastoma patients

  94 sample with multi-omics analysis of ALT-positive neuroblastoma tumors, rna sequencing

  Dataset EGAD00001006587

• RNA data for EGAS00001004660

  RNA data for EGAS00001004660, "Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin"

  Dataset EGAD00001006539

• sc-RNA and sc-BCR sequencing of multiple myeloma and precursors

  bam files of sc-RNA and sc-BCR sequencing of multiple myeloma and precursors from 65 samples

  Dataset EGAD00001009648

• Single-cell RNA sequencing of anti-LAG3+anti-PD1 treated melanoma patients

  Single-cell RNA sequencing of 18 peripheral blood samples from six melanoma patients. The raw data is available as fastq files.

  Dataset EGAD00001009807

• Human Embryonic Multi-tissue ChIP-seq (Manchester)

  Dac EGAC00001000999

• Ig-seq celiac disease Data Access Committee

  Dac EGAC00001001208

• HDBR exome-seq data access committee

  Dac EGAC00001002703

• Whole Transcriptome Sequencing of Human Tumor Cells and Hematopoietic Stem and Progenitor Cells During Aging and Bone Marrow Disorders

  Whole transcriptome sequencing analyses were performed on human hematopoietic stem and progenitor cells during aging and bone marrow disorders. For this purpose, normal and diseased bone marrow or peripheral blood-derived mononuclear cells were FACS-purified into hematopoietic stem (CD34+CD38-Lin-) or hematopoietic progenitor (CD34+CD38+Lin-) populations. Primary human samples from healthy individuals were used along with comparative analyses in some pre-malignant and malignant conditions, including myelodysplastic syndrome (MDS), acute myeloid leukemia (AML) and plasma cell dyscrasias (e.g., multiple myeloma). Studies were also performed on total mononuclear cell fractions from patients with newly-diagnosed or relapsed multiple myeloma, or plasma cell leukemia. Briefly, RNA was extracted from all samples and quality was assessed using a Bioanalyzer instrument. Only samples with RNA integrity (RIN) values >7 were subjected to library preparation for RNA-sequencing. The SMARTer v4 cDNA amplification kit was used along with library construction by the NEB Ultra DNA kit for Illumina. Paired-end sequencing was performed on Illumina NextSeq instruments (Scripps Next Generation Sequencing Core), with all samples run over two separate flow-cells (to generate additional sequencing reads); >95M reads were generated in total for each sample. The RNA-sequencing data are available as FASTQ files.

  Study phs002291

• A capture methyl-seq protocol with improved efficiency and cost-effectiveness using pre-pooling and enzymatic conversion

  The opportunities for sequencing-based methylome analysis of clinical samples are increasing. To reduce its cost and the amount of genomic DNA required for library preparation, we aimed to establish a capture methyl-seq protocol, which adopts pre-pooling of multiple libraries before hybridization capture and TET2/APOBEC-mediated conversion of unmethylated cytosine to thymine. We compared a publicly available dataset generated by the standard Agilent protocol of SureSelect XT Human Methyl-Seq Kit and our dataset obtained by our modified protocol, EMCap, that adopted sample pre-pooling and enzymatic conversion. We confirmed that the quality of DNA methylation data was comparable between the two datasets. As our protocol, EMCap, is more cost-effective and reduces the amount of input genomic DNA, it would serve as a better choice for clinical methylome sequencing.

  Study JGAS000605

• Ribosomal profiling on Epstein-Barr virus transformed B-lymphoblastoid cell lines

  Epstein-Barr virus-transformed B-lymphoblastoid cell lines from six individuals (HG00114, HG00282, NA12005, NA12044, NA12717 and NA12751) of the GEUVADIS Project were selected for ribosomal profiling. For each EBV-LCL, 20 million cells were treated with 2 μg/ml harringtonine and 100 μg/ml cycloheximide. After lysing cells in lysis buffer supplemented with 100 μg/ml cycloheximide, ribosome complexes were purified by density purification. Small RNA molecules were isolated using the NucleoSpin miRNA Kit (Bioke, Leiden, Netherlands), followed by RNA PAGE gel separation. Universal linkers were added after dephosphorylation. After reverse transcription, the cDNA was circularized and, after ribosomal RNA depletion, barcoded and sequenced on Illumina NextSeq 500.

  Dac EGAC50000000209

• Spinocerebellar ataxia type 3 RNA-sequencing study

  RNA-Sequencing from human post-mortem Spinocerebellar ataxia type 3 patients. This sequencing experiment was carried out to validate that the transcriptional changes of an Ataxin-3 knock-in mouse model (expressing an expansion of 304 CAG/CAAs either heterozygous or homozygous in the murine Ataxin-3 locus) represent that transcriptional changes seen in the human disease.

  Study EGAS00001004241

• DIPG RNA and exome sequencing

  DIPG is a paediatric high-grade glioma that diffusely infiltrates the brainstem and is the leading cause of paediatric brain tumour death. Here we performed RNA and whole exome sequencing on DIPG and control samples to analyse transcriptomic and genetic alterations associated with this devastating disease, and to understand the relationship between them.

  Study EGAS00001004749

• 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.

  Study EGAS00001007954

• Transcriptomic data of a discordant monozygotic twin pair for ALS

  The dataset contains bulk RNAseq data of a discordant monozygotic twin pair for ALS; in particular the matrix with gene names and TPM counts for each sample. For both healthy and ALS twin, RNA sequencing was performed on RNA samples collected at two different time points (T1 and T2), for a total of seven samples. RNA extracted from PBMCs was used for library preparation according to Illumina TruSeq Stranded mRNA kit and processed on Illumina NextSeq 550 sequencer. Reads were aligned to the reference human genome GRCh38/hg38 and annotations were provided by the Ensembl v100 database.

  Dataset EGAD50000001330

• RNA sequecing of primary B cells infected with Epstein-Barr virus (EBV) or stimulated with heat-inactivated EBV

  Naïve (CD27-IgD+) B cells were isolated from buffy coat preparations of healthy donors using CD19 magnetic beads, followed by reals of CD19 beads and incubation with IgD-biotin and anti-biotin magnetic beads. B cells were infected with EBV by spinoculation or stimulated with heat-inactivated EBV and control cells were left uninfected. RNA was extracted immediately after isolation in un-infected B cells. From EBV-infected B cells and B cells stimulated with heat-inactivated virus, RNA was extracted 24 and 96 hours after infection / stimulation.

  Dataset EGAD50000000305

• RNA sequencing data of pediatric T-cell acute lymphoblastic leukemia (set 1)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one T-ALL patient (ALLK-118) and from a relapse sample from bone marrow of one T-ALL patient (ALLT-317). Data from the diagnostic sample and relapse sample from tonsil of the ALLT-317 patient are in set 2 of this submission. TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic and relapse tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002584

• GATA1 scD&D-seq integrated with Multiome

  Ex vivo differentiation experiments were performed using human CD34+ hematopoietic stem and progenitor cells along the erythropoietic trajectory at multiple timepoints (differentiation days 0, 5, 8, 18, and 24). Simultaneous profiling of transcriptome, chromatin accessibility, and GATA1 binding were performed by integrating D&D-seq with 10X Multiome.

  Dataset EGAD50000002299

• BLUEPRINT release August 2014, Bisulfite-Seq for Plasma cell

  Bisulfite-Seq data for 1 Plasma cell sample(s). 11 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001000927

• BLUEPRINT release August 2014, Bisulfite-Seq for inflammatory macrophage

  Bisulfite-Seq data for 3 inflammatory macrophage sample(s). 38 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001000914

• BLUEPRINT release August 2014, Bisulfite-Seq for erythroblast

  Bisulfite-Seq data for 1 erythroblast sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001000909

• BLUEPRINT release August 2014, Bisulfite-Seq for macrophage

  Bisulfite-Seq data for 1 macrophage sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001000923

• BLUEPRINT release January 2015, Bisulfite-Seq for erythroblast

  Bisulfite-Seq data for 2 erythroblast sample(s). 35 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001133

• BLUEPRINT release January 2015, Bisulfite-Seq for inflammatory macrophage

  Bisulfite-Seq data for 3 inflammatory macrophage sample(s). 38 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001139

• BLUEPRINT release January 2015, Bisulfite-Seq for plasma cell

  Bisulfite-Seq data for 1 plasma cell sample(s). 11 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001160