12050 results for "cancer rna-seq"

in 14.85 milliseconds.

• Combined DNA Methylation and Genotyping via scTAMARA-seq (DNA)

  This dataset features single-cell DNA methylation and nuclear genotyping data obtained using the scTAMARA-seq protocol, a combination of SDR-seq and scTAM-seq. The targeted panel, 200 DNA methylation (a subset of the orginal 448 CpG targets) and 167 genotyping targets, were applied to a CD34+ enriched bone marrow sample from patient X.1. The data was generated on the Mission Bio Tapestri platform.

  Dataset EGAD00001015496

• H3K27Ac ChIP-seq of 9 cHL cell lines

  The dataset contains 36 ChIP-seq data for H3K27Ac and their corresponging inputs for 9 cHL cell lines. Data are raw paired-end fasq files for each histone and input, and for each cell line.

  Dataset EGAD50000001272

• ChIP-seq peaks of H3K27ac

  ChIP-seq peaks of H3K27ac. The dataset includes FASTQ files, BAM files, and analyses of the ChIP-seq peaks of H3K27ac determined using MACS2

  Dataset EGAD00001008964

• Medulloblastoma Cirlce-Seq

  Circle-Seq experiment.

  Dataset EGAD00001009483

• dataset_CML_chipseq_pairend_bam

  BMI1 ChIP-seq on human K562

  Dataset EGAD00001002062

• dataset_CML_chipseq_pairend_fastq

  BMI1 ChIP-seq on human K562

  Dataset EGAD00001002061

• CATNON: IDH-mutant astroctyoma RNA FASTQ

  Raw fastq files obtained by RNA sequencing 138 IDH-mutant astrocytomas included in the CATNON trial. RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue blocks using the RNeasy FFPE kit. RNA sequencing was performed on an Illumina NovaSeq 6000 (GenomeScan BV, Leiden, The Netherlands) with 150bp paired-end reads including UMI tags.

  Dataset EGAD50000000558

• Bulk RNA sequencing of ALS patients

  We performed RNA sequencing to screen for alternative splicing alterations in patients with ALS to identify those linked to ALS pathology.

  Study JGAS000851

• RNA Sequencing of paediatric patients with B lymphoblastic leukemia

  RNA sequencing was performed on 148 Bone marrow of peripheral blood samples of paediatric patients with B-ALL.

  Study EGAS00001004532

• Simultaneous Trimodal Single Cell Measurement of Transcripts, Epitopes, and Chromatin Accessibility Using TEA-Seq

  Single-cell measurements of cellular characteristics have been instrumental in understanding the heterogeneous pathways that drive differentiation, cellular responses to signals, and human disease. Recent advances have allowed paired capture of protein abundance and transcriptomic state, but a lack of epigenetic information in these assays has left a missing link to gene regulation. Using the heterogeneous mixture of cells in human peripheral blood as a test case, we developed a novel scATAC-seq workflow that increases signal-to-noise and allows paired measurement of cell surface markers and chromatin accessibility: Integrated Cellular Indexing of Chromatin Landscape and Epitopes (ICICLE-seq). We extended this approach using a droplet-based multiomics platform to develop a trimodal assay that simultaneously measures Transcriptomics (scRNA-seq), Epitopes, and chromatin Accessibility (scATAC-seq) from thousands of single cells, which we term TEA-seq. Together, these multimodal single-cell assays provide a novel toolkit to identify type-specific gene regulation and expression grounded in phenotypically defined cell types.

  Study phs002316

• RNA sequencing reads

  Paired-end, ribosome depleted, total RNA Sequencing

  Dataset EGAD00001004327

• A single-cell multi-omic atlas of nodal B-cell non-Hodgkin lymphomas

  CITE-Seq (cellular indexing of transcriptomes and epitopes) of 51 lymph node (LN) samples from including mantle cell lymphoma (MCL, n = 8), follicular lymphoma (FL, n = 12), germinal center (GCB, n = 5) or activated B-cell (non-GCB/ABC, n = 7) diffuse large B-cell lymphoma (DLBCL), and marginal zone lymphomas (MZL, n = 11), in addition to non-malignant reactive lymph nodes (rLN, n = 8). Of the malignant LN samples, 20 were collected at the time of initial diagnosis and 23 were from patients who had previously undergone one or more lines of systemic treatment. Relapse samples were collected at least 3 months after cessation of systemic treatment. This dataset also includes 5 prime RNA sequencing and immune receptor sequencing (10X Genomics) for 11 of these samples (2 rLN, 2 MCL, 3 FL, 2 DLBCL (GCB) and 2 MZL).

  Dataset EGAD50000000497

• RNA-Seq data_MM study cohort (n=73) and human myeloma cell lines

  Multiple myeloma (MM) represents approximately 10 % of all hematological malignancies and patients present with a variety of clinical manifestations and diverse cytogenetic backgrounds While MM patient survival has greatly improved due to novel treatments in the last years, the disease is generally considered incurable with a median survival of approximately 6 years. Therapy resistance remains as a major obstacle, causing almost all patients to eventually relapse, underlining the persisting need to identify novel therapeutic targets and biomarkers associated with disease progression.

  Study EGAS50000000392

• Longitudinal single-cell transcriptomic study in patient-derived xenografts of pediatric T-ALL

  In this study, we conducted single cell full length total RNA sequencing (VASA-seq) on 13 matched pediatric T-ALL PDX samples at initial diagnosis and relapse, along with 5 non-relapsing PDX samples collected at initial diagnosis. We identified a subpopulation of T-ALL cells with stem-like cell features that expands substantially at relapse indicating resistance to first-line therapy. Chemotherapy resistance was further validated through functional testing: Two samples were subjected to in-vitro drug testing, treated with Cytarabine for three days, followed by single-cell transcriptomic analysis using 10x Genomics. Additionally, in-vivo drug testing was conducted on one sample, involving re-engraftment into mice and treatment with a combination of Vincristine, Doxorubicin, and Dexamethasone. Single-cell transcriptomic analysis using 10x Genomics was performed after 0, 15 and 30 days of treatment.

  Dataset EGAD50000000831

• Patient tumour data (RNAseq, WGBS, ChIPseq, WGS)

  Content: 60 GB patient tumours and 4 normal brain samples combined in pairs by region (x2=8 total input samples). RNAseq: 1 lane per sample, total strand-specific rRNA-depleted (normal samples were combined = 2 lanes/samples per brain region). WGBS: 2 lanes per sample (normal samples were combined = 2 lanes/samples per brain region). ChIPseq (histone mark): a subset of 20 GB samples were profiled. For the same modification were multiplexed and sequenced on 4 lanes each (H3K27ac, H3K4me1) or a single lane (all others). WGS: used as matching input control for the 20 ChIPseq samples. Data type and technology: RNA-seq: PE 100bp sequenced on HiSeq2000. WGBS: PE 100bp sequenced on HiSeq2000/4000. ChIPseq: SE 50bp sequenced on HiSeq2000/4000. WGS: PE 150bp sequenced on HiSeq X.

  Dataset EGAD00001005492

• RNA-seq dataset

  RNAseq FASTq files from 728 bulk pre-treatment tumors from IMvigor010.

  Dataset EGAD00001007575

• A Multi-Omic Single-Cell Atlas of Human Gynecological Malignancies

  Matched single-cell transcriptomic sequencing (scRNA-seq) and single-cell chromatin accessibility sequencing (scATAC-seq) were performed for 11 fresh human tumors collected from the endometrium or ovary. More detailed information for each patient tumor will be provided in selected phenotype/attributes data. Both scRNA-seq and scATAC-seq assays revealed the underlying cellular heterogeneity in transcriptional output and in chromatin accessibility for each patient tumor specimen. In this work, we identified potential non-coding regulatory elements that mediate cell type-specific gene expression patterns. These data will serve as an important reference for the single-cell genomics and gynecologic oncology research communities.

  Study phs002340

• Circulating RNA profiles of healthy and preeclamptic pregnancies

  This prospective study investigated whether circulating RNA (C-RNA; cell free RNA present in the bloodstream) measurements could non-invasively monitor pregnancy status, with emphasis on detecting molecular markers associated with preterm preeclampsia. Whole blood samples were collected from pregnant women at the time of diagnosis with early-onset preeclampsia with severe features. Blood samples were also obtained normotypical control pregnancies and from patients diagnosed with late-onset preeclampsia for comparison. For all samples, C-RNA was extracted from 4 mL blood and whole transcriptome enrichment performed on cDNA libraries prior to sequencing to a target depth of 50M reads on an Illumina HiSeq 2000 platform. Throughout the course of this work, whole transcriptome RNA sequencing data was obtained from 289 C-RNA samples collected from 178 subjects. The complete dataset consists of samples from the following cohorts: Illumina Preeclampsia Cohort (iPEC): 40 pregnancies at the time of early-onset preeclampsia diagnosis and 73 gestational age-matched controls PEARL preeclampsia cohort: 12 early-onset and 12 late-onset preeclampsia patients PEARL healthy control cohort: 152 longitundinal samples collected from 41 healthy pregnancies

  Study phs002017

• Metagenomic Analysis to Identify Novel Infectious Agents in Systemic Anaplastic Large Cell Lymphoma

  Anaplastic large cell lymphoma (ALCL) is a rare T-cell non-Hodgkin lymphoma (NHL). Risk of systemic ALCL is markedly increased among immunosuppressed people, such as those with human immunodeficiency virus (HIV) infection or solid organ transplant recipients. This increased risk in immunosuppressed populations suggests a viral etiology, given similar elevations for diffuse large B-cell lymphoma (DLBCL), Burkitt lymphoma, and Hodgkin lymphoma (caused by Epstein-Barr virus [EBV]) and other virus-related cancers in immunosuppressed individuals. EBV might be a plausible candidate, but most reported ALCL tumors are EBV-negative. Therefore, we conducted a metagenomic analysis of microbial associations with ALCL to determine whether a known or novel pathogen is associated with the tumor. We obtained archived formal fixed paraffin embedded (FFPE) ALCL tumor tissue from the Iowa cancer registry and an additional case from an immunosuppressed individual infected with human immunodeficiency virus. Controls included 3 diffuse large B-cell lymphomas (DLBCLs) in transplant recipients (shown to be related to Epstein-Barr virus [EBV] by in situ hybridization) and 3 breast cancers (no known viral etiology). RNA was extracted from FFPE specimens, and total RNA libraries were prepared using the KAPA RNA HyperPrep Kit (Roche). Five samples (IA01, IA53, IA57, IA07, and IA17) were sequenced on a NextSeq 500 (Illumina) and the remainder on a NovSeq 6000 (Illumina). Using novel computational approaches, we eliminated human reads and aligned residual non-human reads to known microbial references using GATK-PathSeq or conducted de novo assembly of unassigned reads using virID pipeline. Although EBV was detected in the 3 DLBCL controls, we did not detect EBV or any novel pathogen in ALCL tumors or in the breast cancers. Our study had a modest sample size and only one case arising in HIV-infected individual. Therefore, further studies are required to characterize the metagenome of systemic ALCLs, especially cases arising in immunosuppressed people.

  Study phs002064

• Characterization of Macrophage-Tropic HIV Infection of Central Nervous System Cells and the Influence of Inflammation

  In this study, we utilize macrophage-tropic and T cell-tropic HIV-1 Env proteins to establish accurate infection profiles for multiple CNS cells under basal and interferon alpha (IFN-α) or lipopolysaccharide (LPS)-induced inflammatory states. We found that macrophage-tropic viruses confer entry advantages in primary myeloid cells, including monocyte-derived macrophages, microglia, and induced pluripotent stem cell (iPSC)-derived microglia. Following 24-h IFN-α or LPS treatments, total RNA was harvested from 100,000 to 200,000 cells using an RNeasy RNA isolation kit (Qiagen, 74004). RNA was quantified using a NanoDrop spectrophotometer and TapeStation electrophoresis prior to library preparation. cDNA libraries were prepared using the KAPA RNA HyperPrep kit (Roche, 08098115702). Paired-end RNA sequencing was performed on a NovaSeq S4 platform at a read length of 100 bp, resulting in approximately 60 million reads per sample.

  Study phs003306

• ChIP-seq and Hodgkin lymphoma

  ChIP-seq data (H3K4Me3, H3K27Ac histone modifications) of Hodgkin lymphoma cell line L-428. Samples were processed as previously described (Sud et al., 2018). The files are in bam format, aligned to build 37 of the human genome.

  Dataset EGAD00001004322

• Functional Multiomics of Cellular Therapy and Immune Checkpoint Blockade Therapy for Solid Tumors

  Tumor samples were collected from a patient with synovial sarcoma, which acquired resistance to ACT targeting NY-ESO-1. Biopsies (n=3; primary, metastasis, and recurrence) were subjected to bulk tumor DNA and RNA sequencing, as well as high-dimensional spatial profiling of RNA and protein targets. Bulk tumor whole exome and RNA sequencing corresponding to all three tumor specimens and whole exome sequencing from patient-matched normal blood are made available through this accession.

  Study phs002762

• Extracellular microRNA Biomarkers for Diagnostic and Prognostic Assessment of Preeclampsia at Triage

  This study is comprised of samples from 123 donors (71 cases and 52 controls) undergoing evaluation for preeclampsia. All samples were collected between 20 and 40 weeks of gestation. Small RNA sequencing was done on serum RNA obtained from donors. We were able to identify 3 bivariate extracellular miRNA biomarkers that can enable early diagnosis of preeclampsia. The raw fastq small-RNA sequencing fastq files will be submitted to dbGaP.

  Study phs003169

• RNA-sequencing on thyroid samples from fetuses with Down syndrome and fetuses with no genetic/developmental abnormality

  The current data pertains RNA-sequencing reads obtained from thyroid samples acquired from fetuses with Down syndrome and fetuses with no genetic/developmental abnormality. Total RNA was isolated from left lobe from thyroid samples using a hand-held homogenizer and the Promega ReliaPrep RNA Miniprep System (Thermo Fisher Scientific). RNA yield was determined with the NanoDrop Microvolume Spectrophotometer (Thermo Fisher Scientific). Fragmentation and mRNA library preparation was performed using the Kapa mRNA Hyperprep Kit (Roche, Basel, Switzerland). Libraries were equimolar pooled and quality was checked on a TapeStation system using the DNA1000 ScreenTape (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced with poly(A) selection to sequence all messenger RNA for gene expression analysis on the NovaSeq6000 PE150 (Illumina, San Diego, CA, USA), producing at least 40M 150-bp paired-end reads per library.

  Dataset EGAD50000000387

• RNA sequencing from patient-derived intestinal organoids

  uman duodenal tissues for establishing organoid cultures used in this study were sourced from de-identified surgical specimens (n = 3) of the duodenum obtained from patients who had undergone biopsy procedures unrelated to CeD at Tampere University Hospital. The protocol was approved by the Ethics Committee of Tampere University Hospital, Tampere, Finland (ETL code R18082). RNA from the duodenal organoids was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. RNA purity and concentration were measured using a NanoDrop One spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA). Preparation of the RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Cambridge, UK). Messenger RNA was purified from total RNA using polyA selection and subjected to library construction. Sequencing was performed on an Illumina platform, and 150 bp paired-end reads were generated.

  Dataset EGAD50000000492