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• Four lymphoma cell lines (AGO2-PAR-CLIP)

  PAR-CLIP was performed on the Argonaute-2 protein (AGO2) in four lymphoma cell lines:NamalwaRajiSU-DHL-4SU-DHL-6

  Dataset EGAD00001001468

• Whole-genome sequencing (WGS) data of Gastric adenocarcinoma and adjacent normal tissues

  High-coverage WGS sequencing of DNA samples from 51pairs GCs was performed on the Illumina HiSeq X Ten System.

  Dataset EGAD00001003392

• Whole-genome sequencing (WGS) data of Gastric adenocarcinoma and adjacent normal tissues

  High-coverage WGS sequencing of DNA samples from 23pairs GCs was performed on the Illumina HiSeq X Ten System.

  Dataset EGAD00001003405

• Epi-Tax targeted sequencing

  Sequencing of 350 cancer genes in BC samples from patients treated with either Epirubicin or Paclitaxel monotherapy in the neoadjuvant setting.

  Dataset EGAD00001000812

• Congenital Heart Disease - Pilot

  This pilot study aims to generate pilot data to inform future study designs by resequencing the whole exomes of 10 unrelated individuals diagnosed with Congenital Heart Disease (CHD).

  Dataset EGAD00001000351

• Fecal 16S UC sequencing data

  Fecal 16S-V4 rRNA gene sequence data from NCT02749630 ulcerative colitis patients. Stool samples were collected at screening as well as on days 29, 43, 64, 85, and 134 processed for 16SV4 rRNA gene sequencing

  Dataset EGAD00001008818

• RNAseq data

  Bulk RNAseq of sigmoid colon biopsies from healthy volunteers and ulcerative colitis patients. Subjects were treated with Placebo or IL-22Fc at different doses, and biopsies were collected at day 0 and day 30 post treatment and prepared for RNA sequencing.

  Dataset EGAD00001008816

• Evolutionary trajectories and clonal migration underlying tumor progression and lymph node metastasis in resectable lung cancer

  In this prospective study, targeted deep sequencing was performed on a total of 160 primary tumors (474 regions) and 112 lymph nodes from 125 patients with stage I-III lung cancer (LuCaTH). Progressive evolution at clonal divergence scale was observed while specific driver events were positively selected for clonal sweeps during tumor development. Between-region genetic divergence (BRGD) of tumors were assessed and positively correlated with tumor differentiation. A machine learning algorithm was employed to evaluate clinicopathological and molecular parameters of primary tumors underlying lymph node metastasis. By analyzing clonal lineages and metastatic trajectories across multiple nodal stations, we unraveled a common sequential LNM seeding pattern but with divergent modes of clonal spread.

  Dataset EGAD00001007587

• The Dutch Microbiome Project Batch 1

  The Dutch Microbiome Project (DMP) data includes shotgun metagenomic sequencing of faecal samples 8,208 Dutch individuals. Paired-end sequencing was performed using Illumina HiSeq 2000 platform. Data is archived in two batches to facilitate easier data access and upload to EGA. Batch 1 of DMP includes 4396 samples.

  Dataset EGAD00001007027

• Access to public datasets in the EGA

  Dac EGAC00001000514

• WGS sequencing of an ES tumor sample

  This Datasets contains whole genome sequencing data of one ES tumor sample. Sequencing was performed on Illumina NovaSeq 6000. The sequencing was paired in bulk.

  Dataset EGAD00001015607

• WES of Multiple myeloma/MGUS cases (germline) - Fastq files

  WXS - Exome capture using the Twist Human Core Exome Kit on germline DNA, paired-end (2x100bp) sequencing on a NovaSeq system. Number of samples: 295

  Dataset EGAD50000001799

• Nanopore targeted sequencing of the CFTR gene in Moroccan patients with suspected cystic fibrosis

  This dataset contains fastq files sequencing with Oxford Nanopore (MK1C)

  Dataset EGAD50000002062

• PBAT sequencing of human embryonic stem cells

  To assess the DNA methylation landscape of naïve human embryonic stem cells derived from ERKi or control blastocysts using PXGL or UXGL media.

  Dataset EGAD50000001475

• RNAseq data of brain metastasis samples

  Paired-end RNA sequencing data from 95 brain metastasis samples with different primary origins. Sequencing was performed on the Illumina HiSeq 3000.

  Dataset EGAD50000000799

• H3K27ac ChIPseq of cohesin-mutated and wildtype adult AMLs

  ChIP-seq targeting the H3K27ac histone modification in cohesin-mutated (STAG2 or RAD21 mutation) and cohesin wildtype (CTRL-AMLs) AMLs.

  Dataset EGAD00001011204

• Single-cell dissection of the immune response after a myocardial infarction

  38 STEMI patients at hospital admission, 24 hours (acute phase) and 6-8 weeks (chronic phase) after STEMI

  Dataset EGAD00001010064

• Pancreatic organoid - case samples

  This dataset contains 31 pancreatic organoid samples used in the 'organoid data of pancreatic cancers ' study

  Dataset EGAD00001004528

• HDAC inhibitor quisinostat in synovial sarcoma cell lines

  An RNA Seq study of the effects of HDAC inhibitor Quisinostat on six different synovial sarcoma cell lines

  Dataset EGAD00001003810

• Bone Cancer - Rare Types Whole Genome

  We propose to definitively characterise the somatic genetics of a selection of rare bone cancers through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Dataset EGAD00001000785

• Exome sequencing of Bilateral Anophthalmia cases- Pilot Study

  This pilot study aims to generate pilot data to inform future study designs by resequencing the whole exomes of 10 unrelated individuals diagnosed with Bilateral Anophthalmia.

  Dataset EGAD00001000348

• A108757B

  Whole genome sequencing for single cells for library A108757B 1644 cells; filetype=bam

  Dataset EGAD00001007086

• Integrated Genetic and Pharmacologic Interrogation of Rare Cancers

  Due to the paucity of patient derived models in rare cancers, identification of therapeutic targets remains challenging. We developed a patient derived model, CLF-PED-015-T, from a patient with an undifferentiated sarcoma. From this model, we performed pooled RNAi and CRISPR-Cas9 negative selection screens and integrated that with a small molecule screen. Integration of these data identified CDK4 and XPO1 as potential therapeutic targets.

  Study phs001121

• Genomic Analysis of Nucleic Acid Sequences from Pancreatic Cancer

  Our study aims to perform multi-omics analysis of pancreatic ductal adenocarcinoma. We performed dual single-cell RNA sequencing and whole genome sequencing on fresh tumor specimens and dual bulk RNA-sequencing and 16S amplicon sequencing on frozen tumor specimens to identify human and non-human nucleic acid sequences. Additionally, we identified microbial sequences and found that bacterial taxonomic profiles from the same sample strongly correlated across technologies.

  Study phs003035

• Non-Coding Mutations Cause Enhancer Targeting Resulting in Protein Synthesis Dysregulation During B-Cell Lymphoma Progression

  In this study, we performed whole-genome sequencing of longitudinal tumor pairs, representing transformation of follicular lymphoma (FL) to high grade B-cell lymphoma with MYC and BCL2 rearrangements (known as "double hit lymphoma" or DHL), a very aggressive class of non-Hodgkin B cell lymphoma (B-NHL). We identified coding and noncoding genomic alterations acquired during the course of lymphoma progression.

  Study phs003398

• Single-Cell RNA-Sequencing of Bone Marrow and Circulating Tumor Cells from Patients with Multiple Myeloma and its Precursor Conditions

  We performed single-cell RNA and V(D)J-sequencing of tumor cells from bone marrow and peripheral blood specimens and patients with Monoclonal Gammopathy of Undetermined Significance (MGUS), Smoldering Multiple Myeloma (SMM), and Multiple Myeloma (MM), as well as healthy donors. In this study we aimed to shed light on the mechanisms underlying tumor cell circulatory capacity and dissemination.

  Study phs003855

• Transcriptomic profiling of myeloid cells from secondary lymphoid organs (lymph nodes and tonsils) from lymphoma patients and controls.

  Despite their recognized impact on the pathogenesis and prognosis of B-cell lymphoma, tumor-associated macrophages (TAM) have not been extensively explored in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). We investigated mononuclear phagocyte (MNP) heterogeneity using single cell RNA sequencing (scRNAseq) in B-cell lymphoma lymph nodes compared to reactive secondary lymphoid organs (lymph nodes and tonsils).

  Study EGAS50000001135

• HipSci___Whole_Exome_sequencing___Usher syndrome and congenital eye defects

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Usher syndrome and congenital eye defects.

  Study EGAS00001001985

• Comprehensive molecular portrait reveals genetic diversity and distinct molecular subtypes of small intestinal neuroendocrine tumors

  This study aims to characterize neuroendocrine tumors of the small intestine (siNETs) from genomic, transcriptomic, epigenomic, and clinical perspectives. Involving 122 patients and 219 samples, we generated whole-genome sequencing data, RNA sequencing data, genotyping arrays, and methylation arrays to conduct an integrative analysis of this rare tumor type. Our findings identify distinct molecular subtypes that correlate with siNET clinical features.

  Study EGAS50000000642

• Discriminating Th17.1 cell driven sarcoidosis-like inflammation from relapse after anti-BCMA CAR T cells in multiple myeloma

  We present a case study on sarcoidosis-like flare-up after Idecabtagen Vicleucel (Ide-cel), a BCMA targeting CAR T cell therapy, and identified a Th17.1 driven autoimmune mechanism as the biological underpinning of this phenomenon using single-cell RNA-seq analysis. Furthermore, single-cell RNA-seq allowed to discriminate between immune-mediated changes and true relapse after CAR T cell treatment.

  Study EGAS00001006133

• ProstOmics - DNA methylation v2

  Bulk methylation array data from 32 prostate tissue samples from 8 patients (3 with post-surgery relapse). Methylation data were acquired using the microarray assay Illumina Infinium MethylationEPIC v2.0 Kit. The individual samples have information on patient origin and sample type (cancer, cancer-adjacent field-effect normal or normal sample far from cancer). Patient metadata include information of age at surgery, time (months) until reported relapse, pre-surgery PSA and post-surgery T-stage.

  Dataset EGAD50000000606

• ProstOmics - DNA methylation v1

  Bulk methylation array data from 64 prostate tissue samples from 16 patients (5 with post-surgery relapse). Methylation data were acquired using the microarray kit Illumina Infinium MethylationEPIC BeadChip (n=64 ). The individual samples have information on patient origin and sample type (cancer, cancer-adjacent field-effect normal or normal sample far from cancer). Patient metadata include information of age at surgery, time (months) until reported relapse, pre-surgery PSA and post-surgery T-stage.

  Dataset EGAD50000000605

• Variation and transmission of the human gut microbiota across generations - shotgun data

  Variation and transmission of the human gut microbiota across generations - shotgun sequencing data

  Dataset EGAD00001008207

• Pediatric Papillary Thyroid Carcinoma RNA-Seq

  38 PPTCs were sequenced using RNASeq to identify oncogenic variants in driver-unknown tumors and to explore gene expression patterns. RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). Libraries were pooled in equimolar quantities and paired-end sequenced on 2 lanes of a High Throughput Run Mode flowcell with the V4 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate paired-end reads of 126-bases in length.

  Dataset EGAD00001007499

• WTS data of patients diagnosed with angiosarcoma

  Whole-transcriptome sequencing (WTS) of 6 tumor-normal and 6 tumor-only samples from patients diagnosed with angiosarcoma. Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on HiSeq 2500 and HiSeq 3000 (Illumina) with 2x101 bp and 2x151 bp read length, respectively.

  Dataset EGAD00001005367

• WTS data of patients diagnosed with NKTL

  Whole-transcriptome sequencing (WTS) of 36 samples from patients diagnosed with NKTL. Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on HiSeq 2500 and HiSeq 3000 (Illumina) with 2x101 bp and 2x151 bp read length, respectively.

  Dataset EGAD00001005230

• The Chinese University of Hong Kong (CUHK) Circulating Nucleic Acids Research Group (CNARG)

  Dac EGAC00001000078

• RNASeq of Calcoco2 in beta and fat cell lines

  Investigation of the function of Calcoco2 by knocking it down in beta and fat cell lines.

  Dataset EGAD00001008654

• Observational study on the immune responses acquired by COVID-19 convalescent individuals

  We performed whole exome sequencing and microarray genotyping analysis of rare disease A two patients. .....

  Study JGAS000563

• MD Anderson Cancer Center HGSOC LRS Data Access Comittee

  Oxford Nanopore long-read sequencing was performed on six paired tumor-normal samples from patients with high-grade serous ovarian carcinoma. Reads were mapped to the GRCh38 reference genome, incorporating base modification information.

  Dac EGAC50000000597

• WES in Angolan and Cape Verdean triple-negative breast cancer samples

  WES (using the SureSelect Human All Exon V5 + UTRs target enrichment kit) in 23 Angolan and 7 Cape Verdean triple-negative breast cancer samples

  Dataset EGAD50000001482

• Cell targeted amplification sequencing (cta-seq) of scRNA-seq sample

  This data-set contains two sequencing runs of the same scRNA-seq library. Once with and once without cell targeted amplification of transcripts.

  Dataset EGAD50000001338

• HRR gene mutation analysis

  Mutation analysis of cfDNA from urine (stored at various storage conditions) and plasma using the QIAseq HRR panel

  Dataset EGAD50000001586

• Primary human hepatocyte ATAC-seq

  Profiling the chromatin accessibility landscape of cultured primary human hepatocytes (PHH) from three female and three male adult, non-diabetic donors.

  Dataset EGAD50000001751

• RODAM cohort: 16S gut microbiome data

  16S rRNA sequencing data of fecal samples of 1211 RODAM cohort participants in three research sites: rural Ghana, urban Ghana and Amsterdam, the Netherlands.

  Dataset EGAD50000001182

• Raw NGS data of primary AML samples

  Raw NGS data of primary Acute Myeloid Leukemia samples. The libraries were obtained with Sophia Genetics Myeloid Solution kit, targeting 30 genes involved in AML.

  Dataset EGAD50000000506

• RNA-seq data of CRC-PDX tumors after drug treatment

  We obtained bulk RNAseq data of CRC-PDX tumors after administration of drug or vehicle to clarify the mechanisms of action.

  Dataset EGAD50000000849

• WGS data of multiple myeloma

  Dataset containing WGS data from 4 patients with 17 samples with multiple myeloma. The sequencing was always paired and performed using Illumina NovaSeq 6000

  Dataset EGAD50000000437

• Whole Genome Sequencing of tumor and blood from 4 pediatric cases with second malignancies.

  Whole Genome Sequencing (120X) of the two tumors and blood from 4 pediatric cases with second malignancies (12 WGS)

  Dataset EGAD50000000237

• Whole Genome Sequencing of 2 expanded clones from rhabdoid tumor case 3

  Whole Genome Sequencing of 2 expanded clones from a cell line derived from the rhabdoid tumor case 3 (2 WGS 20X)

  Dataset EGAD50000000240