15120 results for "cancer studies using rna-seq"

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• Whole Genome sequencing of colorectal cancer patients (SG-BULK-2)

  Whole Genome sequencing of colorectal cancer patients (SG-BULK-2)

  Dataset EGAD00001008574

• September 2016 data update (bam/fastq/vcf) 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.

  September 2016 data update (bam/fastq/vcf) 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 EGAD00001002724

• Udated data for October 2017 data release 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.

  October 2017 data update (bam/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 EGAD00001003906

• The molecular landscape of colorectal cancer reveals genetic mutations - COCA-CN

  We collected tumor samples and adjacent nomal mucosae from 46 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 EGAD00001003304

• January 2018 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.

  January 2018 data update (bam/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 EGAD00001003962

• June 2017 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.

  June 2017 data update (bam/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 EGAD00001003414

• Trimmed bam-files from whole genome sequencing data from plasma DNA

  Single-end sequencing data (trimmed to 60bp) of 104 plasma samples from donors without tumors (male=50; female=54) were merged and used to establish coverage profiles around the TSS and to establish a gene expression prediction algorithm. Dataset includes merged alignements of low coverage whole genome sequencing from plasma DNA from 50 male, 54 female non-cancer donors. Furthermore, 2 patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.

  Dataset EGAD00001002254

• 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

• Fastq data for whole genome shotgun sequencing 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.

  Fastq data for whole genome shotgun sequencing assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001400

• Fastq data for whole genome bisulfite sequencing 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.

  Fastq data for whole genome bisulfite sequencing assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001312

• 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

• 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

• 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

• Spectrum of Response to Platinum and PARP Inhibitors in Germline BRCA Associated Pancreatic Cancer in the Clinical and Pre-clinical Setting

  Whole genome sequencing data for germline BRCA pancreatic cancer

  Dataset EGAD00001011129

• KiCS cancer panel data for academic and for-profit use

  This data set contains KiCS cancer panel data for academic and for-profit use.

  Dataset EGAD00001009734

• Somatic copy number alterations profiling in non-small cell lung cancer and their correlation with clinical efficacy in first-line treatment

  Genomic data from FFPE tumor samples of 258 patients with non-small cell lung cancer (NSCLC), profiled by shallow whole-genome sequencing (sWGS) at 1x. The study aimed to characterize somatic copy number alterations (SCNAs) and SCNA burden to assess their clinical relevance for patient stratification across different first-line treatments.

  Dataset EGAD50000002322

• European Genome-phenome Archive 15th Anniversary Celebration

  2023 marks the 15th Anniversary of the EGA, jointly managed by the European Bioinformatics Institute (EMBL-EBI) and the Centre for Genomic Regulation (CRG). To mark the occasion, a simultaneous celebration was held in both institutions on the 13th of December 2023. The teams gathered online to play a quiz game and celebrate all the achievements and milestones with two wonderful anniversary cakes. In 2008, the European Genome-phenome Archive was created at the EBI-EMBL in Cambridge to guarantee that human genome and phenome data were available to the international scientific community while data privacy was preserved. The six-person staff at the beginning of the project is now far behind us, with a team that reaches the number of 35 members. Since 2013, the European Bioinformatics Institute and the Centre for Genomic Regulation share responsibility for The European Genome-phenome Archive (EGA). At that time, the EGA had data for about 0,5 petabytes. Currently, the Archive contains more than 12 petabytes. 2023 comes to an end with several good news. The EGA has been renewed as an ELIXIR Core Data Resource. This was announced during the GA4GH 11th Plenary held in San Francisco last September when ELIXIR-Beacon was also confirmed to be a GA4GH Driver Project. Thus, the Beacon API has maintained this title since 2018. What’s more, the first Federated EGA dataset is now live on our website. This year we also launched new services for EGA users in September. By the numbers, in 2023 the EGA counts 2.5 PB archived, 371 studies published, 208 new submitters and 19 active projects in which the team is participating, among others. We look forward to continuing to support your research in 2024!

  Blog 15-anniversary

• Expression profiling of a human endocrine pancreas iPSC model

  Directed differentiation of stem cells offers a scalable solution to the need for human cell models recapitulating islet biology and T2D pathogenesis. We profiled mRNA expression at six stages of an induced pluripotent stem cell (iPSC) model of endocrine pancreas development from two donors, and characterized the distinct transcriptomic profiles associated with each stage. Established regulators of endodermal lineage commitment, such as SOX17 (log2 fold change [FC] compared to iPSCs=14.2, p-value=4.9x10-5) and the pancreatic agenesis gene GATA6 (log2 FC=12.1, p-value=8.6x10-5), showed transcriptional variation consistent with their known developmental roles. However, these analyses highlighted many other genes with stage-specific expression patterns, some of which may be novel drivers or markers of islet development. For example, the leptin receptor gene, LEPR, was most highly expressed in published data from in vivo-matured cells compared to the endocrine pancreas-like cells (log2 FC=5.5, p-value=2.0x10-12), suggesting a role for the leptin pathway in the maturation process. Endocrine pancreas-like cells showed significant stage-selective expression of adult islet genes, including INS, ABCC8, and GLP1R, and enrichment of relevant GO-terms (e.g. “insulin secretion”; odds ratio=4.2, p-value=1.9x10-3): however, principal component analysis indicated that in vitro-differentiated cells were more immature than adult islets. Integration of the stage-specific expression information with genetic data from T2D genome-wide association studies revealed that 46 of 82 T2D-associated loci harbor genes present in at least one developmental stage, facilitating refinement of potential effector transcripts. Together, these data show that expression profiling in an iPSC islet development model can further understanding of islet biology and T2D pathogenesis.

  Dataset EGAD00001002148

• DAC - Comparison of sequencing assays for sensitive detection of circulating tumour DNA in stage IA-IV breast cancer

  Dac EGAC00001002549

• Data Access Committee for data from EGAS00001002864: Genome analysis of oesophageal cancer and Barretts oesophagus

  Dac EGAC00001000863