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• Single-cell RNA-seq Libraries via 10x Genomics and Illumina NovaSeq

  This dataset contains single-cell RNA-seq libraries prepared using the Chromium Single Cell 5' Library & Gel Bead Kit v1.1 (10x Genomics). Cells were partitioned into nanoliter-scale GEMs for barcoding and reverse transcription, followed by amplification and purification of cDNAs. Libraries were sequenced on an Illumina NovaSeq 6000 using 150 bp paired-end reads, ensuring high-resolution transcriptomic profiling.

  Dataset EGAD50000001680

• Immunoglobulin Heavy-Chain locus in Multiple Sclerosis (n=4)

  Peripheral-blood or monocyte DNA from two healthy donors and two individuals with multiple sclerosis were sequenced on a PromethION-2 Solo (P2 Solo) instrument using R10.4.1 flow-cells and the Ultra-Long DNA Sequencing Kit (SQK-ULK114). For each participant we provide FASTQ reads (on-target), and haplotype-resolved assemblies of the complete IGH locus (~1.3 Mb) in FASTA format.

  Dataset EGAD50000001517

• Visium Spatial tramscriptomics data set

  This data set contains raw FASTQ files and processed files of spatial transcriptomics of 6 EMD samples collected from MM patients. The processed files contain the h5 expression matrices, the Image of the Visium slide, and a TSV of spatial coordinates. Patients included in this data set are PT01A, PT01B, PT02, PT03, PT07, PT08, PT09, PT10, and PT11.

  Dataset EGAD50000000336

• Raw data (FASTQ) and processed data (VCF) of 7 patient-derived Sézary Syndrome (SS) cells

  We profile the whole-transcriptome (bulk RNAseq) of 7 patient-derived Sézary Syndrome (SS) cells to identify expression patterns, functional programs and expressed gene mutations that may provide clues on new therapeutic options for SS patients. The libraries were sequenced on NextSeq500 (Illumina) with a paired-end read length of 2x75bp. Raw data (FASTQ) and obtained processed data (VCF) including all called raw variants are available.

  Dataset EGAD50000001646

• Whole genome sequencing data from paired tumor and normal tissue in a cohort of NSCLC patients.

  WGS data for paired tumor and normal tissue from 260 patients in the TRACERx ctDNA study. The patient cohort is comprised of NSCLC patients undergoing surgical resection of their tumour. The patients were then followed up for a median of ~5 years after surgery, and serial blood samples were collected. The WGS data here was generated to inform the manufacture of custom ctDNA panels.

  Dataset EGAD50000001693

• Emirati Phased Diploid Trio-Assemblies (27 Individuals, 54 Assemblies)

  This dataset comprises 27 phased diploid genome assemblies (i.e., 54 haplotypes) from Emirati family trios, provided in FASTA format. Sequencing used PacBio HiFi reads generated on the Revio platform at ≥25× coverage for each parent and offspring. Assemblies were produced with hifiasm (trio mode), then scaffolded with NTLink and reference-guided merging via RagTag against CHM13v2. The collection offers haplotype-resolved references suitable for downstream variant discovery and pangenome analyses.

  Dataset EGAD50000001755

• Innate immune cell subsets are enriched in synovial fluid of ACPA-negative rheumatoid arthritis and characterised by distinct type I IFN gene signatures

  This study provides a detailed comparison of the myeloid cell landscape in the SF of patients with ACPA+ and ACPA− RA, highlighting the unique involvement of type I IFN responses in ACPA− RA.

  Study EGAS50000001260

• WGS dataset for Multimodal antigenic escape to GPRC5D-targeted T-cell engagers in multiple myeloma

  We analyzed the genome of plasma cells collected from bone marrow samples or plasmocytoma from patients prior to (when available) and progression on anti-GPRC5D T cell engagers. Dataset includes tumor and matched normal WGS data aligned to GRCh38.p14 in bam format, as well as tumor small variant and CNV calls.

  Dataset EGAD50000001643

• DNA sequencing of sgRNAs in CRISPR-Cas9 screening and RNA sequencing of SF3B4-overexpressing liver organoids

  The dataset contains 18 samples. It includs 12 paired whole genome sequencing, and 2 matched short read and long read RNA sequencing of liver organoids, 2 paired RIP RNA sequencing samples. All the experiments were performed on Illumina platform with raw reads stored in fastq format or bam format.

  Dataset EGAD50000001625

• Clinical Utility of Breast cancer Research by Inocras, Catholic university hospital and Samsung medical center

  Breast cancer remains a major global challenge. To comprehensively characterize its genomic landscape and clinical significance, we analyzed whole genome sequences from 1,364 clinically annotated breast cancers, integrating transcriptome data from most of the tumors.

  Study EGAS50000001062

• Analysis of lymphocytes specific gene expression pattern by RNA-Seq in patients with IgG4-related disease: Comparison between submandibular glands and peripheral blood

  We compared the gene expression of PanT and CD19+B cells by RNA-Seq between SMGs versus PBMCs in IgG4-RD, or IgG4-RD versus pSS versus HCs in PBMCs.

  Study JGAS000630

• colorectal_epigenome

  Three different types of samples were used: 19 normal adjacent, 17 adenoma and 19 colorectal tumor tissue samples. This included 10 pairs of colorectal cancer and normal samples and 1 pair of adenoma-normal samples of the same patient. Tissue specimens were formalin-fixed paraffin-embedded (FFPE). DNA was isolated using the QIAamp FFPE Tissue kit (Qiagen, Hilden, DE) according to the manufacturer’s instructions. The processed DNA was run on the Illumina Human MethylEPIC® v1.0 BeadChip array.

  Dataset EGAD00010002726

• B cells (CD19) RNAseq dataset of JIA patients with known uveitis status.

  CLUSTER consortium RNA sequencing dataset from UK JIA patient cohort with documented uveitis status. Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples and cryopreserved. Samples were subsequently thawed and flow-sorted for CD19+ B cells prior to RNA sequencing. Clinical metadata includes patient demographics and uveitis status at time of sampling.

  Dataset EGAD50000001616

• RNAseq of human intestinal epithelial cell layers cultured in OGM, ENR, and ENRRT

  This dataset contains RNA sequencing data in fastq and bam format from 24 samples of human jejunum organoids grown in 3D configuration or as 2D monolayers on anodisc imaging chambers (AICs) in medium formulations OGM, ENR, and ENRRT. The RNA sequencing samples were sequenced using paired-end sequencing (2x150 bp) on an Illumina NovaSeq 6000 instrument at the SciLifeLab National Genomics Infrastructure (NGI) in Uppsala.

  Dataset EGAD50000001766

• Intrapatient tumor heterogeneity and clonal evolution in metastatic salivary gland cancer: an autopsy study

  This data contains DNA sequencing data of an autopsy study in patients with salivary gland cancer. Whole-genome sequencing was performed on multiple spatially separated tumor samples per patient (4-7 per patient) and healthy control samples.

  Study EGAS50000001420

• Comprehensive molecular and clinicopathological profiling of desmoid tumors

  Previous studies have not clearly identified a prognostic factor for desmoid tumors (DT). Whole-exome sequencing and/or RNA sequencing were performed in 64 cases of DT to investigate the molecular profiles in combination with the clinicopathological characteristics.

  Study JGAS000270

• STimage: Robust and interpretable prediction of gene markers and cell types from spatial transcriptomics data

  This dataset comprises raw sequencing data (FASTQ files) derived from 13 Formalin-Fixed Paraffin-Embedded (FFPE) melanoma tissue samples profiled using the 10x Genomics Visium platform. These spatially resolved transcriptomic profiles serve as the primary dataset for the STimage study, enabling the development and benchmarking of deep learning models that predict gene expression directly from H&E histology images.

  Dataset EGAD50000002172

• Clinical Utility of Breast cancer Research by Inocras, Catholic university hospital and Samsung medical center

  Breast cancer remains a major global challenge. To comprehensively characterize its genomic landscape and clinical significance, we analyzed whole genome sequences from 1,364 clinically annotated breast cancers, integrating transcriptome data from most of the tumors.

  Study EGAS50000001377

• Ankara Bilkent City Hospital Clinical Research Ethics Committee

  Ankara Bilkent City Hospital Clinical Research Ethics Committee is responsible for the oversight and management of access to genomic and phenotypic data generated by the IDH1 Somatic Mutation Profile in Intrahepatic Cholangiocarcinoma . The committee reviews applications for data access to ensure that the proposed research is consistent with the informed consent provided by participants and meets ethical standards. Access is granted to qualified researchers for non-commercial research purposes upon signing a Data Access Agreement (DAA).

  Dac EGAC50000000940

• 10X snMultiome (ATAC+GEX) for the study of "SPEN loss drives extra-follicular diffuse large B cell lymphoma with female-specific lethality and TLR pathway therapeutic vulnerabilities"

  10X snMultiome (ATAC+GEX) sequencing of 1 human reactive tonsil sample and 1 DLBCL sample for the study of "SPEN loss drives extra-follicular diffuse large B cell lymphoma with female-specific lethality and TLR pathway therapeutic vulnerabilities"

  Dataset EGAD50000002277

• Case Report: Pre-Clinical Combination Targeting VEGF and PI3K in a Rare, Aggressive Mixed Endometrial Carcinoma

  We report a rare case of a young patient (VENUS 167) initially diagnosed with grade 1 endometrioid endometrial cancer, which, following endocrine treatment, presented with mixed aggressive carcinoma with three distinct histologic patterns: grade 1 endometrioid, large cell neuroendocrine, and undifferentiated carcinoma. The NGS fastq data are WES, RNAseq and ATAC

  Dataset EGAD50000002397

• BAM-format HiFi whole genome sequencing reads (PacBio Revio) from stabilized human saliva

  HiFi whole‑genome sequencing data from a single human saliva sample collected and stabilized using an Oragene device. Sequencing was performed on a SMRT® Cell using PacBio Revio™ SPRQ chemistry. Sequencing produced >100 Gb of HiFi reads yielding >30× genome coverage suitable for comprehensive variant and methylation analysis. Dataset includes long‑read HiFi sequences in BAM format, containing both aligned and unaligned reads.

  Dataset EGAD50000002398

• Tumor/Normal WXS and RNASeq from patients dosed with neoTCR T-cell therapy

  Sixteen patients with refractory solid cancers received up to three distinct neoTCR-transgenic cell products, each expressing a patient-specific neoTCR, in a cell dose-escalation, first-in-human phase 1 clinical trial (NCT03970382). Included are the tumor and normal WXS and tumor RNAseq for dosed patients.

  Dataset EGAD00001009830

• Transcriptome profiling (RNA-seq) of human acute leukemias

  Total RNA-seq of blasts derived from 131 adult T-ALL cases, 7 AML cases and 1 mixed myeloid/lymphoid leukemia with CpG Island Methylator Phenotype (CIMP). The other RNA-seq data used in this study has been previously published and is available at EGAD00001007581 (AML) and EGAD00001007646 (CD34+ cells).

  Dataset EGAD00001011054

• Single RNA-Seq of CD11b Beads selected tumor associated macrophages (TAMs) of 3 gliomablastoma patients treated with small molecule inhibitors

  Single RNA-Seq of CD11b Beads selected tumor associated macrophages (TAMs) of 3 gliomablastoma patients treated with small molecule inhibitors. The sequencing was done on HiSeq 4000 with the SmarTer Ultra Low Input RNA v4 and NEBNext ChIP-Seq Kit. The TAMs were treated with GW2580, BLZ945 and PLX3397 and DMSO as control.

  Dataset EGAD00001011273