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• Investigating differential diagnostic and prognostic biomarkers in primary cutaneous follicle center lymphoma and follicular lymphoma using low-coverage whole-genome sequencing

  In this study, we analyzed 28 primary cutaneous follicle center lymphoma samples from 20 patients and compared the copy number profiles to a cohort of diagnostic samples of 64 nodal follicular lymphoma patients using low-coverage whole genome sequencing (lcWGS).

  Study EGAS50000000141

• Impact of allogeneic umbilical-cord derived mesenchymal stromal cells on B-cell scRNAseq in patients with systemic lupus erythematosus

  The impact of MSC(UC) on peripheral B cells from Systemic Lupus Erythematosus (SLE) patients was studied by 10X scRNAseq. This scRNAseq study encompassed 3 SLE patients at 3 time points: before or after (1 month, and 3 months) MSC injection in order to analyze B cell subsets and their DEG. The aim of this study was to observe the potential changes of B cell subsets after MSC(UC) injection in SLE patients.

  Dataset EGAD50000000471

• Multi-omics Profiling of Airway Neutrophils and Microbiome in Stable Bronchiectasis

  This dataset comprises raw sequencing data generated from a multi-omics study investigating airway neutrophils and the microbiome in patients with stable bronchiectasis. Samples consist of multiplexed pools derived from blood and sputum collected from multiple subjects. Each pool represents a combination of biological materials from different individuals, and therefore individual-level metadata such as sex and disease stage are not attributable at the sample level. The dataset aims to characterize immune and microbial profiles associated with chronic airway inflammation in bronchiectasis.

  Dataset EGAD50000002607

• Assessment of genomic copy number alterations in breast cancer

  The aim of this study was to assess genomic copy number alterations in a panel of breast cancer cell lines. These data were used to identify common aberrations associated with breast cancer, and also to identify aberrations associated with response to therapeutic compounds.

  Study EGAS00001000585

• Signatures of Aristolochic Acid Mutagenesis in Bladder Cancer

  This study looks at signatures of Aristolochic Acid mutagenesis in bladder cancer, based on exome and whole genome sequencing data. Thirteen bladder tumors and their matched normal DNAs were sequenced on Illumina platforms. Among them eleven were exome sequenced and two were whole genome sequenced.

  Study EGAS00001000975

• Genetic dysregulation of gene expression and splicing during a ten-year period of human aging in the PIVUS study

  We performed RNA sequencing in whole-blood from the same individuals from the PIVUS study at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging.

  Study EGAS00001003583

• Signatures of mismatch repair deficiency in cancer genomes

  DNA replication errors occurring in mismatch repair (MMR) deficient cells persist as mismatch mutations and predispose to a range of tumors. Here, we sequenced the first whole-genomes from MMR-deficient tumors and observed that mutation rates were drastically increased relative to MMR-proficient endometrial tumors.

  Study EGAS00001000182

• 120 individuals from the TEENAGE study (Ntalla et al., 2013) have been genotyped on the Illumina HumanCoreExome-12v1-1_A array. This is a population-based study of adolescents from the Attica region in Greece

  120 individuals from the TEENAGE study (Ntalla et al., 2013) have been genotyped on the Illumina HumanCoreExome-12v1-1_A array. This is a population-based study of adolescents from the Attica region in Greece

  Study EGAS00001001733

• We performed whole exome sequencing (WES) using Hiseq on 22 paired CMLs. We also performed whole exome sequencing (WES) using CG on 88 paired CMLs. All the data belongs to CML in China - ICGC project.

  We performed whole exome sequencing (WES) using Hiseq on 22 paired CMLs. We also performed whole exome sequencing (WES) using CG on 88 paired CMLs.All the data belongs to CML in China - ICGC project.

  Study EGAS00001001742

• Single-cell sequencing of gammadelta and CD8+ alphabeta TCR sequences from blood and gut in coeliac disease

  Single-cell sequencing of gammadelta and CD8+ alphabeta TCR sequences from blood and gut in coeliac disease, before and during gluten challenge (Samples from baseline, day 6 and day 14 blood, and from baseline + day 14 gut). (Paired end, amplicon sequencing).

  Study EGAS00001004484

• Multiplexed quantification of four neuroblastoma DNA targets in a single droplet digital PCR reaction

  Evaluation of quadruplex ddPCR-based copy number assessment in blood plasma samples paired with genomic DNA from the corresponding primary neuroblastoma from three patients and comparison with copy numbers determined by duplex and triplex ddPCR and re-analyzed from whole-exome sequencing (WES) data.

  Study EGAS00001004275

• Amplicon sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study".

  Amplicon sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study". These are Illumina amplicon deep sequencing libraries (n = 118) to validate somatic predictions made in the whole genome sequencing libraries. Specifically, there are 72 tumor libraries and 46 normal libraries. Some patients may have multiple amplicon libraries sequenced.

  Dataset EGAD00001002896

• Genetic control of naive B cell receptor gene usage in celiac disease

  We have characterized the BCR repertoire of naïve B cells in 102 individuals with CeD and 102 control subjects by undertaking gene usage quantitative trait loci analyses based on BCR repertoire sequencing and single nucleotide polymorphism genotyping within the IGH, IGK and IGL loci.

  Study EGAS50000001881

• RSV infection of primary bronchial epithelial cells in asthma

  Primary bronchial epithelial cells derived from healthy donors and asthma patients were differentiated in Air-Liquid-Interface condition and infected with the respiratory syncytial virus. Single-cell RNA sequencing analysis of these cultures was used to study the transcriptomic response of the cells to RSV.

  Study EGAS00001007450

• Mesothelioma Whole Genomes

  Genomic architecture of mesothelioma parent study is project 925. This project is set up in parallel to project 925 in order to Whole genome sequence ten of the 59 tumours in that project.

  Dataset EGAD00001001265

• Analysis of tumor periphery and center-specific mutations in renal cell carcinoma

  Renal cell carcinoma (RCC) is a genomically heterogeneous tumor. In the present project, the question whether intratumoral heterogeneity follows a zonal pattern indicating spatial niches was addressed. Whole exome sequencing of 16 paired samples from tumor periphery and center revealed a number of region-specific functional SNVs and Indels. Therefore, RCCs are not composed of evenly admixed tumor cells but show topological differences in their clonal composition.

  Dataset EGAD00001002067

• DNA-seq BAM files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by HPAH

  Paired-end DNA-seq BAM files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by hereditary pulmonary arterial hypertension (HPAH). Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). FASTQ files were processed at the CNAG (Barcelona) using the GEM short-read aligner on the human genome version hs37d5, producing a total of 16 BAM files.

  Dataset EGAD00001005757

• subset of DEEP IHEC release 2016 (EGAS00001001937), as used in EGAS00001001656 (bidirectional promotors paper, Fatemeh et al. 2018)

  part of the DEEP project results resulted in the publication of 'Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters', Epigenetics & Chromatin (2018), Fatemeh et al., DOI: 10.1186/s13072-018-0236-7, PMID: 30414612, PMCID: PMC6230222. This dataset contains the subset of DEEP data related to that study.

  Dataset EGAD00001005953

• RNA-seq bulk

  This dataset gather all RNA-sequencing data in MM.1S cell line in control and Dex condition; both in 3 biological replicates

  Dataset EGAD00001011137

• Combining dasatinib and IFN-α in CML – immunomodulatory effects linked to treatment response and adverse events

  We pooled 100,000 cells from the 12 scRNA+TCRab-seq samples from peripheral blood from three time points (n=4, samples at 0, 3, and 12 months) to understand the landscape of immune subsets in CML during the course of dasatinib+IFN-α treatment

  Study EGAS00001005049

• Array-based DNA methylation analysis in blood from patients with Snijders Blok–Campeau syndrome (CHD3)

  DNA methylation array data generated using the Illumina Infinium MethylationEPIC BeadChip (v1.0 and v2.0) from whole-blood DNA of patients with Snijders Blok–Campeau syndrome (ORPHA:599082). Raw IDAT files were generated to identify differentially methylated regions in typical and atypical patients.

  Study EGAS00001008414

• HNPCC-Sys: Molecular Characterization of Lynch Syndromes

  Lynch Syndrome (LS) tumors are characterized by constitutional mutations in DNA mismatch-repair genes. Colorectal cancers (CRCs) are the predominant tumor type in patients with LS. Here, we have used whole-genome and transcriptome sequencing of LS- CRC to find similarities and differences of mutation and gene expression characteristics between LS-CRC and sporadic CRC (data provided by TCGA via dbGaP). Furthermore, we were interested in the molecular heterogeneity of LS-CRC. We have performed a molecular characterization of LS-tumors and of matched tumor-distant reference colonic mucosa based on whole-genome DNA- and RNA-sequencing analyses. Our data indicates the existence of two subgroups of LS-CRCs, G1 and G2, where G1 tumors show a higher number of somatic mutations, higher microsatellite slippage and a different mutation spectrum.

  Study phs001407

• International Genetics of Parkinson Disease Progression (IGPP) Consortium: EPIPARK and HBS2 Cohorts

  EPIPARK and HBS2 cohorts were analyzed as part of the International Genetics of Parkinson Disease Progression (IGPP) Consortium. EPIPARK is a population-based cohort to study non-motor symptoms in parkinsonism in the city of Lübeck, Germany led by Drs. Meike Kasten and Christine Klein. HBS2 is a recently enrolled subset of participants in the Harvard Biomarkers Study led by Dr. Clemens Scherzer (www.bwhparkinsoncenter.org/biobank) of 89 participants with a diagnosis of Parkinson Disease (PD). Genotyping with Illumina Infinium Multi-Ethnic Genotyping Arrays (MEGA chip) was performed by Dr. Scherzer, Harvard Medical School and Brigham and Women’s Hospital. 179 participants with a diagnosis of PD from EPIPARK and 89 participants with a diagnosis of PD from HBS2 met Q/C criteria were analyzed.

  Study phs002328

• RNA-Seq from PMM2-CDG Patients and Healthy Controls

  Besides the predominant neurological involvement of PMM2-CDG patients, around 20% of patient mortality has been linked to severe infections. However, the immunological dysfunction in PMM2-CDG is not well understood. In this study, we aimed to address this gap and study the molecular mechanisms affected behind immunological issues in PMM2-CDG. Primary skin fibroblasts from three PMM2-CDG patients and three healthy controls were stimulated or not with TNF-alpha and their gene expression was assessed by RNA sequencing. The response to TNF-alpha was characterized based on the differential expressed genes and functional enrichment and and compared between PMM2-CDG and healthy individuais. Gene expression alterations and functional enrichment were further validated by several experimental assays by ELISA, Flow Cytometry and Western Blotting.

  Study phs003313

• Single cell multi-omics analysis of chromothriptic medulloblastoma highlights genomic and transcriptomic consequences of genome instability

  Chromothripsis is a form of genome instability, whereby a presumably single catastrophic event generates extensive genomic rearrangements of one or few chromosome(s). However, little is known about the heterogeneity of chromothripsis across different clones from the same tumor, as well as changes in response to treatment. We analyzed single-cell genomic and transcriptomic alterations linked with chromothripsis in human p53-deficient medulloblastoma (n=7). We reconstructed the order of somatic events, identified early alterations likely linked to chromothripsis and depicted the contribution of chromothripsis to malignancy. We characterized subclonal variation of chromothripsis and its effects on double-minute chromosomes, cancer drivers and putatively druggable targets. Furthermore, we highlighted the causative role and the fitness consequences of specific rearrangements in neural progenitors.

  Study EGAS00001005410