23164 results for "ega"

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• NKI PRECSION copy number lpWGS

  128 samples with DCIS and matched recurrences sequenced with lpWGS

  Dataset EGAD00001008401

• S:CORT Stratification in COloRecTal cancer

  Colorectal cancer samples will be submitted for Illumina sequencing using a custom capture of 116 genes implicated in colorectal tumourigenesis. Driver mutations will be detected and ultimately correlated with phenotypic data.

  Dataset EGAD00001009760

• Whole genome sequencing of malignant pleural mesothelioma

  Whole genome sequence from paired tumour and germline samples from mesothelioma patients

  Dataset EGAD00001008447

• Spatial transcriptomics of 1 untreated prostate cancer.

  Two sections of cryopreserved prostate cancer tissue from one untreated prostate cancer patient were profiled for spatial transcriptomics using the Visium Spatial library preparation protocol from 10x Genomics. The GRCh38 aligned sequencing reads from the two prostate cancer tissue sections are provided as BAM files.

  Dataset EGAD00001007921

• GELATO clinical trial RNA-Seq data (primary tumors and local recurrences)

  RNA-Seq data of 10 lobular breast cancer primary tumors and 3 local recurrences obtained from 11 unique patients from GELATO clinical trial. The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000 from archived FFPE material.

  Dataset EGAD00001009835

• Single Cell Transcriptomic Analysis of Cellular Heterogeneity in Human Colorectal Tumours

  1,591 single cells from 11 colorectal cancer patients were profiled using Fluidigm based single cell RNA-seq protocol to characterized cellular heterogeneity of colorectal cancer. 630 single cells from 7 cell lines were profiled similarly to benchmark de novo cell type identification algorithms.

  Dataset EGAD00001002727

• Differential methylation positions

  This dataset includes an analyzed DMP file that provide the information about differential methylation positions based on Illumina Infinium MethylationEPIC BeadChip. All samples (5 lung cancer cases vs. 5 benign lung disease controls) were obtained from bronchial washings at the site of the lesion under bronchoscopy manipulation. Of the five lung cancer cases, 3 are adenocarcinoma and 2 are squamous carcinoma.

  Dataset EGAD00001010147

• PPGL RNA-Seq dataset

  Dataset includes fastq files for RNA-Seq experiments for tumor samples of PPGL patients. Single end reads fastq files are available for 102 different samples

  Dataset EGAD00001008578

• Peripheral Blood Leukocytes 10x Genomics scRNA-seq

  This dataset contains 10x Genomics Single Cell 3’ Solution (version 2) scRNA-seq data from peripheral blood leukocytes of a single healthy donor. Data from 20939 cells were collected over 8 lanes and 2 sequencing runs.

  Dataset EGAD00001008590

• Whole Exome Sequencing of 5 FFPE prostate samples (normal and tumour pairs) to identify mutations

  Whole Exome Sequencing was performed on radical prostatectomy formalin-fixed paraffin-embedded sample pairs (n = 6). Library prep was done by exon capture using the Illumina Truseq Exome kit and sequenced as 75bp paired end on Illumina NextSeq 500. Sequences were aligned to the human genome (hg38) using BWA.

  Dataset EGAD00001006107

• Single-Cell Protein Expression via scTAMseq Cite-seq

  This dataset contains single-cell surface marker expression profiles generated by integrating the Cite-seq protocol with scTAMseq. Samples were stained with an antibody panel targeting 45 (donor A.6 & A.7) and 56 (donors A.1-A.5, B.1-B.5, and X.2 ) surface proteins to enable robust phenotypic characterization.

  Dataset EGAD00001015497

• Single-cell short-read transcriptomes from CH, MDS and AML patients with splicing factor mutations

  Single-cell RNA sequencing from CH (n = 2), MDS (n = 6, MDS02 in 2 replicates) and AML (n = 1, in 2 replicates) samples with mutations in splicing factors (SF3B1 - n = 8, U2AF1 n = 1). cDNA from 10x Genomics 3' V3.

  Dataset EGAD00001011283

• Low-coverage whole-genome sequencing (lcWGS) data of Genome in a Bottle (GIAB) reference samples

  This dataset contains low-coverage whole-genome sequencing (lcWGS) data generated from three GIAB reference samples (HG001–HG003) for method benchmarking and concordance analysis in FFPE-GWAS workflows. The data were generated using Illumina NovaSeq with paired-end 150bp reads and downsampled to 2x coverage.

  Dataset EGAD00001015533

• Combined Metabolic Activators Reduces Liver Fat in Nonalcoholic Fatty Liver Disease Patients

  Metagenomics data for "Combined Metabolic Activators Reduces Liver Fat in Nonalcoholic Fatty Liver Disease Patients". Samples were sequenced on NovaSeq6000(NovaSeq Control Software 1.7.0/RTA v3.4.4) with a 151nt (Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using ‘NovaSeqXp’ workflow in ‘S4’ mode flow cell.

  Dataset EGAD00001008142

• RNAseq of jejunum (small intestine) harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 or vehicle

  This experiment consists of RNAseq of jejunum (small intestine) harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 (N = 14) or with vehicle (N = 14).

  Dataset EGAD00001009390

• HDBR exome sequencing data (November 2022)

  Exome sequencing data from seven phenotypically abnormal human fetal samples. Anaysis perfomed using Illumina NovaSeq 6000, Twist Bioscience - Human Comprehensive Exome. Paired end fastq files were aligned to hg38 reference genome using BWA-MEM v0.7.15, followed by sorting using SAMtools sort v1.3.1, and duplicate reads marked using Picard Tools MarkDuplicates v2.18.2

  Dataset EGAD00001009715

• Dataset-linking-WGS-via-README-for-EGAS00001004884

  This dataset contains 139 Tumor and Control WGS files for samples for Gerhauser et al.,Cancer Cell, 2018, 34:996-1011. WGS and sequencing protocol was earlier described in Weischenfeldt et al, Cancer Cell, 2013.

  Dataset EGAD00001007669

• Genomic profiling of patient-derived xenograft models of myxoid liposarcoma either sensitive or resistant to trabectedin

  The dataset consists of two patient-derived xenograft model of myxoid liposarcoma one sensitive and one resistant to trabectedin. Both models underwent the same treatment schedule with trabectedin (tree time points and one treatment with doxorubicin). We performed genomic profiling using Agilent OneSeq assay.

  Dataset EGAD00001005099

• Mixture of 4

  Mixture of 4 unrelated individuals sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.

  Dataset EGAD00001008724

• Mixture of 3

  Mixture of 3 unrelated individuals sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.

  Dataset EGAD00001008729

• Novel method for efficient establishment, expansion and drug response profiling of high-grade serous ovarian cancer organoids

  HGSOC patient-derived organoids and their tissue of origin

  Dataset EGAD00001008753

• Pre-neoadjuvant treatment biopsy RNAseq breast cancer dataset

  This dataset contains RNAseq data of n=87 pre-treatment biopsies of triple negative and luminal- type breast cancer patients, all scheduled to receive neoadjuvant chemotherapy. Gene expression data is linked with treatment response and survival.

  Dataset EGAD00001008433

• Dataset for bone_cancer-WHOLE_GENOME

  Rare cancer sequencing data of 48 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008866

• Whole genome sequencing of GM09237 cells with and without folate depletion

  Two DNA samples extracted from GM09237 cell line cultured with either normal medium or medium with no folic acid for 5 days were sequenced using the BGISEQ500 platform (BGI whole genome 100 bp paired-end sequencing 60x) as well as PacBio Sequel long read sequencing.

  Dataset EGAD00001007732

• Whole exome sequencing of patient derived cell lines

  Whole exome sequencing of 3 patients derived cell lines and patient blood (N = 6 samples), performed using Agillent SureSelect All Exon V5 and Illumina HiSeq 4000. Data is in raw fastq format (N = 10 fastq pairs, 20 files total), as some samples were split between two lanes.

  Dataset EGAD00001007738

• BLUEPRINT release August 2016, ChIP-Seq for macrophage - T=6days LPS, on genome GRCh38

  ChIP-Seq data for 2 macrophage - T=6days LPS sample(s). 6 run(s), 6 experiment(s), 6 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 EGAD00001002498

• 20190219_EGA_MelanomaOnTreatment

  Illumina platform sequencing data for matched tumour-normal DNA samples from 77 melanoma patients participating in a study investigating response to immunotherapy. Selected cases also have RNA sequencing of the tumour.

  Dataset EGAD00001004869

• Bulk RNA-sequencing of AML blasts pre and post culture

  This dataset contains 18 Fastq files from 9 samples (pre-culture (n=3), post culture in standard (n=4) or niche-llike (n=2) conditions) from 4 patients.They correspond to bulk RNA sequencing on Illumina instrument of libraries prepared using SMARTer Universal Low Input RNA Kit.

  Dataset EGAD00001008773

• WES on tumor DNA and germline DNA in pediatric cancer

  This dataset contains whole exome sequencing (WES) data (various enrichment methods) from tumor DNA samples of various pediatric cancer entities. Files are provided in fastq format. Samples were sequenced on a Novaseq6000 or Hiseq2500 (Illumina).

  Dataset EGAD00001007816

• RNA-seq of Bone Metastasis from breast and prostate cancers

  RNA-seq of Bone Metastasis from breast and prostate cancer (4 breast and 5 prostate samples). Dataset contains BAM files from RNA-seq performed using Illumina HiSeq 2500.

  Dataset EGAD00001006356

• WGBS analysis corresponding to representative cases of iBCP-ALL patients

  This dataset was conceived to characterize the epigenomic landscape of representative iBCP-ALL subtypes. To do so, we performed Whole Genome DNA bisulfite-sequencing on 2 MLL-AF4, 2 MLL-AF9 and 2 non-MLL rearranged leukemias, and also 2 pools of BCPs obtained from fetal liver.

  Dataset EGAD00001005010

• Small RNA sequencing from CSF extracellular vesicles - PD/CTR

  The dataset contains FASTQ files referring to the study "Small RNA sequencing from CSF extracellular vesicles - PD/CTR". For this project, RNA was isolated from CSF extracellular vesicles obtained by ultracentrifugation. Libraries were prepared with the TruSeq Small RNA library prep Illumina, and sequencing conducted in the Illumina HiSeq4000.

  Dataset EGAD00001006629

• Single cell study of infant leukemias

  We have performed single cell RNA-sequencing for infant and childhood B-cell acute lymphoblastic leukemias as well as infant acute myeloid leukemias at diagnosis. The sequencing was performed with 10X Chromium single cell 3’ and 5’ chemistry.

  Dataset EGAD00001007853

• BLUEPRINT September 2016, ATAC-seq for venous blood, on Genome GRCh38

  ATAC-seq data for 136 sample(s) from venous blood, on Genome GRCh38. 141 run(s), 139 experiment(s), 139 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002709

• 106 mouse cases and 10 human cases

  Consists of 76 mouse plasma cell-free DNA, 30 mouse Liver DNA, 10 human plasma cell-free DNA

  Dataset EGAD00001008838

• Dataset for cancer_of_unknown_primary-EXON

  Rare cancer sequencing data of 62 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008870

• Dataset for GIST-WHOLE_GENOME

  Rare cancer sequencing data of 18 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008876

• Dataset for upper_gastrointestinal_tumor-WHOLE_GENOME

  Rare cancer sequencing data of 28 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008901

• Dataset for synovial_sarcoma-EXON

  Rare cancer sequencing data of 34 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008898

• Paired RNA-Seq of Tumor Organoids from glioblastoma, 2 patients, treated with different small molecule inhibitors

  Tumor Organoids from glioblastoma, 2 patients, treated with different small molecule inhibitors. Paired RNA-Seq was done on NovaSeq 6000 with the Illumina TruSeq stranded mRNA Kit. The small inhibitors GW2580, BLZ945 and PLX3397 were used. DMSO was used as control.

  Dataset EGAD00001011274

• SF11979 scRNA-Seq Primary GBM IDHR132H Wild-type Female

  Single Cell-RNA Seq IDHR132H Wild-type Primary GBM Female, 76. Single Cell RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through cellranger count (10xGenomics.)

  Dataset EGAD00001005390

• SF11136 scRNA-Seq Primary astrocytoma IDH mutant

  Single cell RNA-Seq Primary diffuse astrocytoma G2. IDH mutant, ATRX mutant. Gender Male Age 34. Single Cell RNA seq from primary astrocytoma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005394

• BLUEPRINT release August 2016, DNase-Hypersensitivity for macrophage - T=6days B-glucan, on genome GRCh38

  DNase-Hypersensitivity data for 4 macrophage - T=6days B-glucan sample(s). 4 run(s), 4 experiment(s), 4 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_dnaseseq_analysis_20160816

  Dataset EGAD00001002425

• bulk RNA-Seq samples of CRC patients

  The dataset contains samples of 30 CRC patients (3 samples for each patient, tumor and 2 normal adjacent tissue sites, 90 samples in total). Dataset is composed by fastq file (paired end) type from bulk RNA-Seq.

  Dataset EGAD00001009635

• Tumor mutational burden (TMB) calculated on bladder tumor pre-treatment DNA sequencing data

  Data from NABUCCO cohort 1 (NCT03387761). This dataset includes Tumor mutational burden (TMB) calculated on bladder tumor pre-treatment DNA sequencing data (n=24). Details about the Tumor Mutational Burden calculation can be found on the Methods section from the Nature Medicine paper (https://doi.org/10.1038/s41591-020-1085-z)

  Dataset EGAD00001006851

• RNA-seq TPM matrices

  Matrices of TPM-normalized counts from RNAseq data for the three phase II clinical trials (IMvigor210, POPLAR, IMmotion150) and the phase I clinical trial PCD4989g.

  Dataset EGAD00001006741

• Oropharyngeal Squamous Cell Carcinoma Mutanome

  This dataset comprises genetic variation data (as somatic indels and snvs VCFs) of 38 OPSCC tumors. WES was done using NextSeq 500 System running in 150 cycles (2x 75bp paired-end) mode. Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422. VCFs were generated using the Strelka package.

  Dataset EGAD00001009167

• RNA sequencing of tumor samples from patients with Waldenstrom macroglobulinemia

  RNA was extracted from flow-sorted CD19+. RNA-Seq was performed on 32 samples of 30 patients (2 replicates per samples). RNA-Seq libraries were subjected to non-stranded paired-end (2 x 75 bp) sequencing on HiSeq 2500 (Illumina). The files are in FASTQ format.

  Dataset EGAD00001005324

• ChIP-seq ERa and H3K27ac in endometrial healthy and tumor tissues

  ChIP-seq has been perfomed on 4 healthy and 5 tumor fresh-frozen endometrial tissues from post-menopausal patients. Immunoprecipitation has been performed for H3K27ac and ERa. Raw single-end fastq data have been aligned using bwa-mem using Hg19 genome assebly as reference. Aligment bam files are provided.

  Dataset EGAD00001010896

• RNA-seq data of 370 high grade ovarian tumors from the ICON7 trial

  Collection of RNA-seq, Illumina, paired-end fastq files for 370 archival tissues from a subset of patients with high grade serous ovarian carcinoma enrolled in the phase 3 ICON7 trial. Clinical data and digital pathology information for CD8 is also available.

  Dataset EGAD00001004988