22938 results for "ega"

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• BLUEPRINT release January 2015, ChIP-Seq for effector memory CD8-positive, alpha-beta T cell, terminally differentiated

  ChIP-Seq data for 1 effector memory CD8-positive, alpha-beta T cell, terminally differentiated sample(s). 4 run(s), 4 experiment(s), 4 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_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001195

• BLUEPRINT release August 2016, RNA-Seq for effector memory CD4-positive, alpha-beta T cell, on genome GRCh38

  RNA-Seq data for 2 effector memory CD4-positive, alpha-beta T cell sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002469

• BLUEPRINT release August 2016, RNA-Seq for central memory CD8-positive, alpha-beta T cell, on genome GRCh38

  RNA-Seq data for 1 central memory CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002482

• BLUEPRINT release August 2015, ChIP-Seq for CD4-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 7 CD4-positive, alpha-beta T cell sample(s). 39 run(s), 39 experiment(s), 39 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001505

• Targeted sequencing of genes recurrently mutated in AML - part2

  Genomic libraries will be generated from total genomic DNA derived from 4000 samples with Acute Myeloid Leukaemia. Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 64 Samples will be individually barcoded and subjected to up to one lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.

  Dataset EGAD00001000747

• Processed microarray gene expression data from NPC samples_Cohort 2

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006274

• Whole-exome ultra-high throughput sequencing in brain samples of suicide victims who had suffered from major depressive disorder and control subjects who had died from other causes

  Whole exome NGS data of 21 sucide victims and 23 control patients sequenced on Illumina HiSeq 2000 platform using the Agilent SureSelect Human All Exon + UTRs V5 target enrichment kit. The dataset contains the paired-end unfiltered FASTQ files, the GRCh37 (b37) aligned BAM files mapped by the BWA MEM algorithm, and the variant files in VCF 4.1 format called with the GATK HaploType caller (version 3.3).

  Dataset EGAD00001004184

• Transcriptomic intra-tumor heterogeneity of colorectal cancer evaluated by RNA sequencing of multi-regional biopsies

  RNA sequencing of a total of 41 tumor biopsies taken from a total of 14 patients with colorectal cancer. Ribosomal RNA was removed using the Ribo-Zero Gold rRNA Removal Kit (Illumina, CA, USA) and Paired-end sequencing were performed using ScriptSeq v2 RNA-seq Library preparation Kit (Illumina). Data processing of the paired raw sequence reads was performed using TopHat2, with mapping to the human reference genome HG19. Forty-one BAM files with reads mapping the the human reference genome (HG19) is enclosed.

  Dataset EGAD00001006636

• sWGS of OV04 PDX samples for ACN rascal study

  This dataset contains 148 .bam files of shallow WGS data (~0.1X) from OV04 PDX samples. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008119

• SCLC study George et al. - RNA-sequencing data set

  RNA-sequencing (RNA-seq) was performed with RNA extracted from fresh-frozen human tumor tissue samples. cDNA libraries were prepared from poly-A selected RNA applying the Illumina TruSeq protocol for mRNA. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 30x of the annotated transcriptome.

  Dataset EGAD00001001244

• BLUEPRINT release August 2016, RNA-Seq for CD14-positive, CD16-negative classical monocyte, on genome GRCh38

  RNA-Seq data for 8 CD14-positive, CD16-negative classical monocyte sample(s). 8 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002308

• BLUEPRINT release August 2016, ChIP-Seq for CD3-positive, CD4-positive, CD8-positive, double positive thymocyte, on genome GRCh38

  ChIP-Seq data for 3 CD3-positive, CD4-positive, CD8-positive, double positive thymocyte sample(s). 11 run(s), 11 experiment(s), 11 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002445

• Deep exome sequencing

  Bam files from deep exome sequencing of blood DNA samples from five TET2 mutation carriers (Ly1, Ly2, Ly9, Ly11, Ly14) and three wild-type family members (Ly8, Ly10, Ly13) extracted at multiple time points. Library preparations were performed with SeqCap EZ Exome v3 (Roche, Switzerland) using six different index primers per sample for which paired-end Illumina sequencing was done with 75bp read length and HiSeq4000 sequencer. After alignment (bwa version 0.7.12), base recalibration (GATK 3.5), realignment around indels (GATK 3.5) and duplicate removal (MarkDuplicates; Picard Tools version 1.79), data from libraries with six different indexes were merged.

  Dataset EGAD00001004780

• BLUEPRINT release August 2015, ChIP-Seq for central memory CD4-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 1 central memory CD4-positive, alpha-beta T cell sample(s). 9 run(s), 7 experiment(s), 7 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001499

• Anaplastic Meningioma WGS-X10

  Anaplastic meningiomas are a rare, malignant variant of meningioma. At present there is no effective treatment for this cancer. The aim of the study is to identify somatic mutations in anaplastic meningiomas. We plan to sequence a set of 500 known cancer genes in 50 anaplastic meningioma and corresponding peripheral blood DNA samples. Bioinformatics will be used to analyse the results to assess the probability of these mutations being causal and so likely of critical importance for the tumour growth. Identification of these mutations will guide selection of appropriate compounds to effectively treat the disease.

  Dataset EGAD00001001267

• TIGER samples

  The TIGER samples dataset contains PISA cohort samples which consist of paired RNA-seq and genotyping array data. It contains 127 RNA-seq pair-end samples in fastq format and 127 individuals genotypes in PLINK format.

  Dataset EGAD00001007990

• BLUEPRINT release August 2015, ChIP-Seq for effector memory CD8-positive, alpha-beta T cell, terminally differentiated, on genome GRCh38

  ChIP-Seq data for 1 effector memory CD8-positive, alpha-beta T cell, terminally differentiated sample(s). 4 run(s), 4 experiment(s), 4 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001577

• Gene expression profile of mesothelial-derived carcinoma-associated fibroblasts

  RNA-sequencing was carried out on ascetic fluid-isolated mesothelial cells from low-grade serous ovarian cancer patients, high-grade serous ovarian cancer patients, chemotherapy-treated high-grade serous ovarian cancer patients and control mesothelial cells obtained from non-oncologic patients to identify differentially expressed genes associated to mesothelial-to-mesenchymal transition process. The dataset contains 18 samples: - Control mesothelial cells: 4 samples - Group 1, high-grade serous ovarian cancer patients: 3 samples - Group 2, chemotherapy-treated high-grade serous ovarian cancer patients: 5 samples - Group 3, low-grade serous ovarian cancer patients: 6 samples

  Dataset EGAD00001005133

• Genetic background for the major psychiatric disorders in the general Finnish population

  Low coverage (4-6x) sequencing on samples from population cohorts (Finrisk, Health2000) will be done at Wellcome Trust Sanger Institute (WTSI) using Illumina HiSeq sequencing technology. We will produce 100bp paired end reads. Variants will be called using the 1000 Genomes Project pipeline. The samples have been selected from a national representative set of 8028 samples from persons of 30 years or older, which were screened for psychotic and bipolar disorders using the Composite International Diagnostic Interview, self-reported diagnoses, medical examination, and national registers.

  Dataset EGAD00001001250

• BLUEPRINT release August 2015, RNA-Seq for CD4-positive, alpha-beta T cell, on genome GRCh38

  RNA-Seq data for 10 CD4-positive, alpha-beta T cell sample(s). 10 run(s), 10 experiment(s), 10 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001544

• BLUEPRINT release August 2015, ChIP-Seq for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell, on genome GRCh38

  ChIP-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 7 run(s), 6 experiment(s), 6 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001557

• Molecular and phenotypic data for patients enrolled in the IMmotion150 trial

  Tumor transcriptome and whole exome sequencing data (matched tumor/normal for somatic mutation calling) along with key phenotypic information are provided for patients enrolled in the phase 2 IMmotion150 trial, assessing efficacy of atezolizumab monotherapy or combination of atezolizumab and bevacizumab versus standard of care (sunitinib) in 1L renal cell carcinoma. This data set accompanies the respective Nature Medicine publication (PMID: 29867230).

  Dataset EGAD00001004183

• BLUEPRINT release August 2015, RNA-Seq for CD14-positive, CD16-negative classical monocyte, on genome GRCh38

  RNA-Seq data for 8 CD14-positive, CD16-negative classical monocyte sample(s). 8 run(s), 8 experiment(s), 8 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001506

• Exome sequencing of Congenital Heart Disease families Leuven

  This project aims to study at least 90 exomes from families with congenital heart disease. The samples have been selected in Leuven in collaboration with Koen Devriendt. Ethic approval has been sought for in Leuven, Belgium and a HDMMC agreement for submitting these samples is in place at the WTSI. The phenotype we wil primarily focus our analysis is severe Left Ventricular Outflow Tract Obstructions (LVOTO) and Atrioventricular Septal Defect (AVSD). The indexed Agilent whole exome pulldown libraries will be sequenced on 75bp PE HiSeq (Illumina).

  Dataset EGAD00001000796