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• Immune profiling reveals enrichment of distinct immune signatures in oral epithelial dysplasia

  The dataset contains transcriptomic information of 36 oral potentially malignant disorders (OPMD), 14 fibroepithelial polyps (FEP), and 6 early stage oral squamous cell carcinoma (OSCC) from the Asian population. Total RNA was extracted from formalin-fixed paraffin embedded (FFPE) tissue sections. RNA libraries were prepared using the NEB NextUltra RNA kit with Illumina Ribo-Zero rRNA removal as per manufacturer’s instructions. RNA sequencing was performed on the HiSeq2500 platform to generate paired-end 150 nucleotides reads and with a coverage of 50 million reads per sample. Uploaded bam files have been mapped to the GRCh38 human genome using TopHat2. Clinical and demographic data for these patients are available from the associated publications or by request.

  Dataset EGAD00001007970

• Stage-specific gene and transcript dynamics in human male germ cells

  The testis is one of the most transcriptionallyactive organs, however how germ cell differentiation is controlled at the molecular level remains largely unknown. To study global transcriptional dynamics during human spermatogenesis we sequenced total RNA of human testicular biopsies with 5 specific histological phenotypes: Sertoli cell-only (SCO, n=3), spermatogenic arrests at the spermatogonial (SPG, n=4), spermatocyte (SPC, n=3), and spermatid (SPD, n=3) level, as well as normal spermatogenesis (Normal, n=3). To our knowledge, this work provides the most complete capture of the transcriptome and its dynamics during human spermatogenesis to date.

  Study EGAS00001006135

• Metagenomics-Guided Pathogen Discovery in Travelers' Diarrhea

  Traveler's diarrhea (TD) is caused by enterotoxigenic Escherichia coli (ETEC), other pathogenic gram-negative pathogens, norovirus and some parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 30% of TD patients, so it is predicted that new pathogens or groups of pathogens may be causative agents of disease. A comprehensive metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers was performed, all of which tested negative for the known etiologic agents of TD in standard tests. Metagenomic reads were assembled and the resulting contigs were subjected to semi-manual binning to assemble independent genomes from metagenomic pools. Taxonomic and functional annotations were conducted to assist identification of putative pathogens. We extracted 560 draft genomes, 320 of which were complete enough to be enough characterized as cellular genomes and 160 of which were bacteriophage genomes. We made predictions of the etiology of disease in individual subjects based on the properties and features of the recovered cellular genomes. Three subtypes of samples were observed. First were four patients with low diversity metagenomes that were predominated by one or more pathogenic E. coli strains. Annotation allowed prediction of pathogenic type in most cases. Second, five patients were co-infected with E. coli and other members of the Enterobacteriaceae, including antibiotic resistant Enterobacter, Klebsiella, and Citrobacter. Finally, several samples contained genomes that represented dark matter. In one of these samples we identified a TM7 genome that phylogenetically clustered with a strain isolated from wastewater and carries genes encoding potential virulence factors. We also observed a very high proportion of bacteriophage reads in some samples. The relative abundance of phage was significantly higher in healthy travelers when compared to TD patients. Our results highlight that assembly-based analysis revealed that diarrhea is often polymicrobial and includes members of the Enterobacteriaceae not normally associated with TD and have implicated a new member of the TM7 phylum as a potential player in diarrheal disease.

  Study phs001352

• Dataset contains all Single cell RNAseq data of human neurons from the study Bouwen et al Nat Comm 2025

  These documents contain the patch seq data presented in the Bouwen et al Nat Comm 2025. Human brain samples were gathered during surgery, neurons were isolated using patch clamp glass pipette. Isolated cells were processed using Smartseq2 pipeline, and sequenced using an Illumina 2500. Files are formatted in fastq format. There are a total of 12 patient samples, each with 2 replication runs.

  Dataset EGAD50000001979

• Bulk RNA sequencing data of high-grade serous ovarian cancer samples (set 7-17)

  The dataset contains RNA sequencing data of 272 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000, MGISEQ or Hiseq X Ten. The 814 samples are fresh frozen tissue samples that have been collected from different tissues and time points before and during treatment. The files provided are paired fastq files.

  Dataset EGAD50000001370

• Therapy-related myeloid neoplasms and HSPCs from the International-Berlin-Frankfurt-Münster (I-BFM) Study group

  Dataset contains WGS sequencing data from bulk sorted therapy-related myeloid neoplasms (t-MN) and reference cells (MSCs/B cells/T cells). In addition, from 4 patients, also WGS data from single hematopoietic stem and progenitor cells, obtained from samples of t-MN diagnosis, are included. These are either clonally expanded before WGS, or DNA was directly amplified via the primary template-directed amplification (PTA) protocol (mentioned in the sample name).

  Dataset EGAD00001011256

• Recalibrated whole-exome sequencing alignment data of papillary thyroid cancer of Saudi Arabia

  The dataset consists of samples from papillary thyroid cancer patients. A total of 11 DNA samples from blood/normal and cancer tissue are subjected to whole exome sequencing using Illumina. The fastq files generated were aligned with reference genome ‘hg19’, duplicates were marked, realignment around indels and quality recalibration were performed to produce good quality variants. The recalibrated “.bam” files are included with this dataset.

  Dataset EGAD00001004490

• Heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer

  A mutation accumulation experiment in colorectal cancer (CRC) derived tumoroids. A sequential single-cell cloning approach was adopted to measure the mutation rate in eight tumoroids obtained from five patients. WGS was also performed on their matched normal tissue and on standard tumoroids cultures without any cloning step. This is a 150x depth sequencing for 7 samples.

  Dataset EGAD50000000616

• NABUCCO cohort 2 Whole Exome Sequencing (Tumor and Blood)

  Data from NABUCCO cohort 2 (NCT03387761). This dataset includes Whole exome DNA sequencing on bladder tumor samples matched with blood samples for patients from NABUCCO Cohort 2 (Cohort 2A and Cohort 2B). The data is pre-treatment

  Dataset EGAD00001009864

• Whole exome sequencing of non-small cell lung cancer patient-derived xenografts

  Non-small cell lung cancer (NSCLC) is the leading cause of cancer deaths worldwide. Only a fraction of NSCLC harbour actionable driver mutations and there is an urgent need for patient-derived model systems that will enable the development of new targeted therapies. We generated NSCLC patient-derived xenografts (PDXs) that recapitulate the histology and molecular features of primary NSCLC. Here, we completed whole exome sequencing on 122 NSCLC PDXs.

  Dataset EGAD00001008601