9182 results for "cancer rna-seq"

in 32.80 milliseconds.

• Submission 5 - study_title 1

  Submission 5 - description 1

  Study EGAS50000000284

• Whole-genome sequenicng of 168 paired Gastric Cancer patients (1st part) DAC

  Dac EGAC00001001145

• Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

  Study EGAS00001005472

• Genetics and transcriptomics of human acute erythroid leukemia

  Study EGAS00001004203

• Submission 10 - study_title 2

  Submission 10 - description 2

  Study EGAS50000000073

• Submission 115 - study_title 1

  Submission 115 - description 1

  Study EGAS50000000163

• Childhood B-cell acute lymphoblastic leukemia genomic and transcriptomic data

  Study EGAS00001006863

• LLDeep DAG2+ scRNA-seq in PBMCs

  Single cell transcriptomics of PBMCs of 47 donors from the Lifelines Deep cohort (general population, Northern part of the Netherlands). Cells of five or six different donors were pooled together in one sample pool, resulting in eight different sample pools. In total, 28.855 cells were captured and their transcriptomes were sequenced to an average depth of 74k. Genotype data was available for each donor, which allowed us to use the Demuxlet method that uses variable SNPs between the pooled individuals to determine which cell belongs to which individual. Since genotype information is lacking of 2 individuals, the transcriptome of only 45 individuals could be retrieved.

  Dataset EGAD00010001315

• Whole-exome sequencing of 20 samples of actinic keratosis (10s) and cutaneous squamous cell carcinoma (10s)

  Whole-exome sequencing of 20 samples of actinic keratosis (10) and cutaneous squamous cell carcinoma (10) was performed to investigate a potential relationship between DNA methylation-based subtypes and genetic mutation patterns. 7 samples were shown to belong to the stem cell-like subclass (4 AK and 2 SCC), 12 - to the keratinocyte-like subtype (6 AK and 6 SCC) and one SCC sample is unclassified (was not included in the methylation analysis). Exome regions were captured using Agilent Low Input Exome-Seq Human v5 kit and sequenced on Illumina Hiseq4000 with paired-end 100-nucleotide reads.

  Dataset EGAD00001003765

• 112 "KOREAN" never-smoker female adenocarcinoma exome-seq

  All sequencing was performed within the DNAlink (Korea) by using the Solexa sequencing technology (Illumina, San Diego, CA). 1 ug of genomic DNA was sheared to an average size of 150 bp by using the Covaris System. The libraries were prepared by using TruSeq DNA Sample Prep Kit (Illumina). The purified DNA library was hybridized with the SureSelect Human All Exon V3 probe set (Agilent Technologies) to capture 50 Mb of targeted exons following the manufacturer’s instructions. Exome capture was carried out using the Agilent SureSelect Human All Exon 50Mb Kit. The captured exome libraries were sequenced on the Illumina HiSeq2000 using the manufacturer’s recommended protocols.

  Dataset EGAD00001005126

• mRNA and T cell receptor sequencing of patients with Pandemrix-associated narcolepsy type 1

  PBMCs isolated from 27 individuals (11 narcolepsy type 1 patients, 16 healthy controls) were stimulated with the peptide Neuroaminidase 175-189 or Protein-O-mannosyl transferase 1 (POMT1) 675-689 or media as control. FACS sorted CD4+ and CD8+ lymphocytes from one patient were subjected to the same stimulation. Transcriptome profiling was done with a 3' tagging protocol. T cell receptor repertoires were profiled with amplicon sequencing (Rep-seq). The dataset contains FASTQ files with sequencing reads, transcript count matrices and TCR clonotypes.

  Dataset EGAD00001006797

• mRNA and T cell receptor sequencing of patients with Pandemrix-associated narcolepsy type 1

  PBMCs isolated from 27 individuals (11 narcolepsy type 1 patients, 16 healthy controls) were stimulated with the peptide Neuroaminidase 175-189 or Protein-O-mannosyl transferase 1 (POMT1) 675-689 or media as control. FACS sorted CD4+ and CD8+ lymphocytes from one patient were subjected to the same stimulation. Transcriptome profiling was done with a 3' tagging protocol. T cell receptor repertoires were profiled with amplicon sequencing (Rep-seq). The dataset contains FASTQ files with sequencing reads, transcript count matrices and TCR clonotypes.

  Dataset EGAD00001006796

• Single-cell B-cell receptor sequencing data of peripheral blood mononuclear cells obtained from 30 ATL patients, 11 HTLV-1-infected asymptomatic carriers, and 4 healthy donors.

  Single-cell B-cell receptor sequencing (scBCR-seq) data of peripheral blood mononuclear cells (PBMCs) obtained from 30 ATL patients (34 samples including 4 sequential ones), 11 HTLV-1-infected asymptomatic carriers, and 4 healthy donors.

  Dataset EGAD00001007013

• McGill EMC Community projects Release 7 for cell line "hTERT RPE1"

  Complete reference epigenome (as defined by IHEC) of normal hTERT RPE1 cell line as well as hTERT RPE1 cell lines engineered to express EPC1-PHF1 and JAZF1-SUZ12 fusion proteins, found in Endometrial Stromal Sarcoma.

  Dataset EGAD00001007680

• Single-cell multi-omics analysis of COVID-19 patients with pre-existing autoimmune diseases

  Single-cell analysis of the transcriptome, T cell immune receptors, and surface proteome (CITE-seq) from peripheral blood mononuclear cells (PBMCs) of COVID-19 patients with pre-existing autoimmune diseases (rheumatoid arthritis n = 5, psoriasis n = 4, or multiple sclerosis n = 3), as well as COVID-19 patients without pre-existing autoimmunity as controls (n = 10) to investigate altered immune responses.

  Dataset EGAD00001007982

• ATAC-seq of uncultured CD112high and CD112low long-term(LT) human hematopoietic stem cells (HSC) from umbilical cord blood

  ATAC-sequencing was performed to establish chromatin accessibility signatures that underlie the differential in vitro priming and regeneration phenotypes of CD112high and CD112low LT-HSC. CD112high and CD112low LT-HSC from 2-3 independent human umbilical cord blood pools were prospectively isolated for DNA extraction, library preparation and sequencing.

  Study EGAS00001005121

• Childhood Cancer Survivor Study (CCSS)

  Background and Rationale for the Childhood Cancer Survivor Study (CCSS) Over the last several decades, advances in treatments for childhood and adolescent cancer have substantially improved survival following diagnosis. These improvements gave rise to the responsibility for investigating long-term treatment-associated morbidity and mortality. Early efforts to describe late effects were largely conducted through single-institution and limited consortia studies. However, by the mid-1980s, it became increasingly clear that these approaches had inherent limitations, including small sample size, convenience sampling, incompletely characterized populations, and limited length of follow-up. To overcome these limitations, the CCSS was proposed and funded by the National Cancer Institute (NCI) as a U01 grant in 1994. Subsequently, the strengths of the CCSS, including an efficient and extensive infrastructure, plus expanding database and biorepository, were recognized and appreciated. Thus, in consultation with the NCI, the CCSS was converted to a U24 (resource grant) funding mechanism to serve the scientific community in 2000. The overarching goal of the CCSS resource is to increase the conduct of innovative and high impact research related to pediatric cancer survivorship. CCSS has been used extensively by researchers from a wide range of disciplines to address a broad spectrum of topics. Strengths of the resource include its large size, comprehensive annotation of treatment exposures, ongoing longitudinal follow-up with characterization of a wide array of participant characteristics and outcomes, and an established biorepository. Design of the Childhood Cancer Survivor Study The Childhood Cancer Survivor Study (CCSS) is a multi-institutional, multi-disciplinary collaborative research resource comprised of a retrospective hospital-based cohort of survivors of childhood cancer and a comparison sibling cohort. Eligible survivors from 31 participating institutions were diagnosed between 1970 and 1999, prior to age 21 years, with selected common pediatric cancers (leukemia, central nervous system tumors, Hodgkin lymphoma, non-Hodgkin lymphoma, kidney tumors, neuroblastoma, soft tissue sarcoma, or bone tumors). All patients who survived five years from the date of diagnosis were eligible, regardless of disease or treatment status. The baseline questionnaire was completed by 24,368 survivors and 5,039 siblings recruited to serve as a comparison group. To date, participants have completed three general follow-up surveys, as well as a number of specialized surveys on specific topics (e.g. health care, insurance, screening practices, men's and women's health issues, adolescent health, sleep and fatigue). In addition, biological samples (buccal cells, saliva and/or blood) have been collected for over 11,000 participants. Full descriptions of the design and characteristics of the CCSS have been previously published (Robison et al; Leisenring et al.), and available data and samples are described at https://ccss.stjude.org/develop-a-study/gwas-data-resource.html. Treatment Data in the Childhood Cancer Survivor Study A key feature of CCSS is the availability of detailed treatment data, which were collected by abstraction of medical records for each individual member of the cohort. Detailed abstraction included dates of therapy, protocol information, and specific details regarding surgery, chemotherapy and radiation. Quantitative dose details were collected for 22 specific chemotherapeutic agents, including alkylating agents, anthracyclines, platinum compounds and epipodophyllotoxins. In addition to individual agent doses, algorithms have been created to calculate cumulative doses of all drugs in a specific class, such as anthracyclines (doxorubicin, daunomycin and idarubicin) or platinum agents (cisplatinum and carboplatinum). Data abstracted for surgeries included dates and both the names and corresponding International Classification of Diseases (9th revision) code. For radiation treatment data, all relevant records were sent to the Radiation Physics Center at M.D. Anderson Cancer Center for detailed abstraction and dosimetry. Initial body region dosimetry was performed for all participants, followed by more detailed dosimetry as needed for specific studies. Genomics Data in the Childhood Cancer Survivor StudyThe NCI's Division of Cancer Epidemiology and Genetics and CCSS investigators collaborated to conduct genomics studies (SNP array genotyping and whole exome sequencing) using samples from the CCSS Biorepository. Studies included all cohort participants with available DNA regardless of sex or ancestry when the genomics studies were initiated. Phenotype Data in the Childhood Cancer Survivor Study Vital status and cause of death for both participants and non-participants is determined via linkage with the National Death Index (NDI). Identification of subsequent neoplasms is based on self-report, followed by validation using medical records, or via NDI. A wide array of additional health outcomes have been ascertained via a comprehensive set of questions on the CCSS questionnaires, covering potential adverse events across a range of organ systems (hearing/vision/speech, urinary, hormonal, heart and circulatory, respiratory, digestive, brain and nervous systems). In addition to health outcomes, longitudinal data have been collected on demographics, health behaviors, family history, screening practices, insurance status, and a range of psychosocial and neurocognitive factors. A full listing of available variables and copies of the CCSS questionnaires are available at http://ccss.stjude.org. Research Areas in the Childhood Cancer Survivor Study Extensive use by the research community has resulted in over 265 published manuscripts on a wide range of topics, including associations between treatment factors and mortality, subsequent neoplasms, chronic health conditions, cardiac events, neurocognitive sequelae, psychosocial factors, fertility, and health status. Additional topics have included health behaviors, screening practices, health care access and utilization, statistical and exposure assessment methodology, and development of risk prediction models. A full listing of published manuscripts using CCSS data is available on the CCSS website at https://ccss.stjude.org/published-research/publications.html. The Childhood Cancer Survivor Study as a Resource for Investigators The CCSS is an NCI-funded resource (U24 CA55727) to promote and facilitate research among long-term survivors of cancer diagnosed during childhood and adolescence. Interested investigators are encouraged to develop research ideas and propose projects within CCSS, whether or not they are from a participating CCSS institution. The CCSS is now accepting proposals to collaborate with CCSS and NCI investigators in the use of genomics data and corresponding outcomes-related data to address innovative research questions relating to potential genetic contributions to risk for treatment-related outcomes. Any researcher, or group of researchers, qualified to conduct genetic research can submit a proposal. There are no restrictions relative to country, institution, or prior involvement in CCSS. A full description of the process for developing a proposal for genetic research in CCSS can be found at https://ccss.stjude.org/develop-a-study/gwas-data-resource.html, along with listings of approved proposals.

  Study phs001327

• EGAD00010000526

  SNP 6.0 arrays of small cell lung cancer

  Dataset EGAD00010000526

• Bladder cancer sequencing data

  Dataset EGAD00001001036

• Submission 17 - study_title 1

  Submission 17 - description 1

  Study EGAS50000000021

• Submission 14 - study_title 1

  Submission 14 - description 1

  Study EGAS50000000044

• Low_Coverage_Sequencing_of_rare_human_histiocytic_tumour

  Sequencing of rare human histiocytic tumour

  Study EGAS00001000768

• Primary_angiosarcoma_Whole_Genome_Sequencing

  Whole genome sequencing of primary angiosarcoma

  Study EGAS00001000851

• Sequencing_of_rare_human_histiocytic_tumour

  Sequencing of rare human histiocytic tumour

  Study EGAS00001000591

• RNAseq

  RNAseq of pancreatic cancer organoids.

  Dataset EGAD00001010834

• Submission 80 - study_title 1

  Submission 80 - description 1

  Study EGAS50000000118

• Stromal cell diversity associated with immune evasion in human triple‐negative breast cancer

  Study EGAS00001005061

• Targeted next-generation sequencing of 13 chordoid gliomas of the third ventricle

  Study EGAS00001002733

• Genome-wide DNA Copy Number Analysis of high hyperdiploid acute lymphoblastic leukemia

  Study EGAS00001007049

• Detection of Gene Fusions using Targeted Next-Generation Sequencing – a Comparative Evaluation

  Study EGAS00001004934

• Whole-genome and transcriptome sequencing of blastic plasmacytoid dendritic cell neoplasm

  Study EGAS00001003660

• Organoid Models of Human Liver Cancers Derived from Tumor Needle Biopsies

  Study EGAS00001003115

• Multiscale heterogeneity in gastric adenocarcinoma evolution is an obstacle to precision medicine

  Study EGAS00001004525

• Multi Omics of glioma in the the Chinese Glioma Genome Atlas (CGGA) project

  Study EGAS00001004729

• Mixed Histology Lung Cancers Driven by Transcriptomic Features rather than Genomic Characteristics

  Study EGAS00001005140

• TK-EPN862 - Patient-dervied xenograft model of Posterior Fossa A Ependymoma - WGS

  Study EGAS00001006843

• Barts Cancer Institute - Follicular Lymphoma Whole Genome Sequencing Project Data Access Committee

  Dac EGAC00001000086

• Memorial Sloan Kettering Cancer Center - Human Oncology & Pathogenesis Program (HOOP) - Data Access Committee

  Dac EGAC00001000305

• Functional Genomics Laboratory, Kolling Institute of Medical Research DAC - TP53 mutation data in ovarian cancer

  Dac EGAC00001000589

• The data access committee for genome-wide cell-free DNA fragmentation in patients with cancer

  Dac EGAC00001001180

• Microbiome confounders and quantitative profiling challenge established microbial targets in colorectal cancer developmental stages

  Study EGAS00001007413

• The University of Hong Kong Gastric Cancer Organoids RHO Signaling Study Data Access Committee

  Dac EGAC00001002705

• The genomic imprint of cancer therapies helps timing the formation of metastases

  Study EGAS00001003416

• National Cancer Institute (NCI) Adding Hispanics to Ongoing GWAS in Colorectal Cancer

  Genome-wide association studies (GWAS) of colorectal cancer (CRC) have been instrumental in identifying a number of common susceptibility loci in Non Hispanic (NH)-White populations, and a NCI priority is to extend GWAS findings to other populations to address racial/ethnic disparities in cancer susceptibility. Currently, GWA studies of CRC in NH-Whites, Japanese and African-Americans are ongoing. We propose a complementary study to address this critical research area in Hispanics. Hispanics represent the fastest growing ethnic population in the U.S. and have been largely understudied in terms of genetic susceptibility to cancer. There are noted differences in incidence, survival and mortality in CRC by ethnic/racial groups. Hispanics often present with CRC at a younger age and have a significantly greater incidence of stage IV tumors or metastatic disease compared to NH-Whites. We propose to conduct a large, cost-efficient, population-based GWAS in Hispanics by building upon existing NIH-funded resources, the Colon Cancer Family Registry (Colon CFR) and the Multiethnic Cohort Study (MEC). We plan to recruit 2,500 Hispanic men and women diagnosed with CRC between 01/2008 to present using cancer registries in California, physican referrals and familial referrals. Risk factor/diet questionnaires, pathology reports, Oragene saliva samples (for genotyping), optional blood samples (for genotyping and biometric analysis) and tumor blocks (for MSI testing) will be collected using methodologies developed in the Colon CFR/MEC. Cases of CRC in the MEC (currently 473; anticipated 600 at end) will also be included. Population-based Hispanic individuals without a diagnosis of CRC participating in other GWA studies in the MEC (n=3,900, U01HG004726, Haiman) will be used as controls. We will genotype all 3,100 cases using the Illumina 1M array and use available genotype and epidemiologic data collected on 3,900 controls. Our statistical analyses will include: single-SNP and haplotype effects, gene-environment interactions and heterogeneity by MSI, tumor subtype and family history of CRC. We will replicate findings in a second-stage using CRC cases and controls from Mexico (1,000 cases and 1,000 controls, EU FP7 funding, CHIBCHA, Carvajal-Carmona/Tomlinson). We will also examine heterogeneity of the risk estimates by ethnicity/race by leveraging GWA data on NH-Whites (2,142 cases, 1,909 controls, U01 CA122839, Casey), (4,000 cases, 6,000 NH-White controls, UK-CHIBCHA, Tomlinson), Colombians (2,000 cases and 2,000 controls, CHIBCHA), Japanese (1,000 cases and 1,000 controls) and African-Americans (1,500 cases and 1,500 controls, R01CA126895, Le Marchand). We will genotype replicated significant SNPs in our main and combined analysis in several Hispanic populations (note: studies funded by EU or NIH for data collection but not GWAS), including 800 Puerto Ricans, 2,000 Brazilians, 2,000 Argentineans and 3,000 Spanish/Portuguese, to assess generalizability of findings. We will examine the differences in inflammatory gene transcription dynamics in leukocytes (from blood sample collection) by fatigue level (as assessed from study questionnaire data). This study will have a high impact by addressing the key question of racial/ethnic disparities related to genetic susceptibility to CRC, will provide translational guidelines on biological mechanisms during the cancer survivorship period to increase quality of life among cancer survivors, and will enable further growth and investment into research among Hispanics by providing a resource of genetic data and biospecimens, which is lacking.

  Study phs001193

• Japanese RIKEN liver cancer WGS

  RIKEN collection of WGS reads for 269 liver cancer tumors and matched normal blood or liver tissue from 258 donors. In total there are 1864 paired fastq sets sequenced on Illumina HiSeq 2000 or Genome Analyzer II instruments with paired reads of 75–101 bp. Quality control and duplication removal has not been performed.

  Dataset EGAD00001001881

• March 2016 update of Whole genome bisulfite sequencing assay data (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of Whole genome bisulfite sequencing assay data (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001957

• March 2016 update of Whole genome bisulfite sequencing assay data (bams) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of Whole genome bisulfite sequencing assay data (bams) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001987

• December 2016 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  December 2016 data update (bam/fastq for WGBS on samples CEMT0062, CEMT0068, CEMT0072, CEMT0086, CEMT0087) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001003122

• The molecular landscape of colorectal cancer reveals genetic mutations（5 cases）

  We collected tumor samples and adjacent nomal mucosae from 5 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing.

  Dataset EGAD00001003223

• The molecular landscape of colorectal cancer reveals genetic mutations（17 cases）

  We collected tumor samples and adjacent nomal mucosae from 17 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing.

  Dataset EGAD00001003224