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• Single-cell RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015713

• Determining off-target effects of splice-switching antisense oligonucleotides using short read RNAseq in neuronally differentiated human induced pluripotent stem cells

  Neuronal cells derived from female healthy control hiPSC lines LUMCi003-A, LUMCi003-B and LUMCi023-A were transfected with in total four different splice-switching AONs targeting three different human transcripts. Untransfected samples as well as samples transfected with a scrambled AON were included as controls. Three days after transfection, RNA was isolated for sequencing using Illumina Novaseq6000 in order to perform differential gene expression analysis and differential splicing analysis to determine off-target effects. Sequencing was performed in two batches: one containing the samples from cell line LUMCi003-A and the other containing cell lines LUMCi003-B and LUMCi023-A.

  Dataset EGAD50000001742

• Characterization of Macrophage-Tropic HIV Infection of Central Nervous System Cells and the Influence of Inflammation

  In this study, we utilize macrophage-tropic and T cell-tropic HIV-1 Env proteins to establish accurate infection profiles for multiple CNS cells under basal and interferon alpha (IFN-α) or lipopolysaccharide (LPS)-induced inflammatory states. We found that macrophage-tropic viruses confer entry advantages in primary myeloid cells, including monocyte-derived macrophages, microglia, and induced pluripotent stem cell (iPSC)-derived microglia. Following 24-h IFN-α or LPS treatments, total RNA was harvested from 100,000 to 200,000 cells using an RNeasy RNA isolation kit (Qiagen, 74004). RNA was quantified using a NanoDrop spectrophotometer and TapeStation electrophoresis prior to library preparation. cDNA libraries were prepared using the KAPA RNA HyperPrep kit (Roche, 08098115702). Paired-end RNA sequencing was performed on a NovaSeq S4 platform at a read length of 100 bp, resulting in approximately 60 million reads per sample.

  Study phs003306

• Controlling cell differentiation with precision through understanding the structure and dynamics of gene regulatory networks

  We established a set of transgenic human ES cell lines that carry inducible expression gene cassette for singe transcriptional factor induction with Tet-ON system. Transcriptome data was obtained 48h after transgene induction by Microarray. We established inducible human ES lines about more than 700 genes, and achieved microarray analysis on 115 genes. Our data set has multiple characteristic properties; 1) the same platform across data set, 2) analyzed with dynamic cell status, 3) pre-determined initiation point on gene perturbation, 4)inducible in different cell status. In parallele, we also performed RNA sequenncig analysis on 435 transgene induced ES lines as well. 32 transgene induced transcriptome data were obtained from both Microarray and RNA sequencing, normalizing technical gaps between them. We hope those systematic data set to reveal transcriptional network structure and molecular mechanisms of cell differentiation.

  Study JGAS000121

• Transcriptome analysis of a novel human iPSC-derived 3D cortical tissue model - WT, APP KI, Abeta-treated, Abeta/Aducanumab-treated

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model. Samples include distinct conditions (each as biological duplicates): - wild-type cells from cultures after 1 month (WT_1mo, cell lines: A18, KOLF) and 3 months (WT_3mo, cell lines: SA2, KOLF, A18) of culturing - knock-in cells from cultures carrying three familial AD mutations in the APP gene (Swedish, Iberian, Arctic; introduced by CRISPR/Cas9-mediated knock-in) after 3 months of culturing (KI_3mo, cell lines: SA2, A18) - subset of WT 1 month-old samples were exposed to 500nM synthetic Abeta42 for 2 consecutive feeds, and a subset of these subsequently treated with 1µg/ml Aducanumab antibody for 14 days

  Dataset EGAD50000002031

• Transcriptome of memory B cells with autoproliferation in MS

  Transcriptional profile of resting/hi and autoproliferating/Dim memory B cells in Multiple sclerosis patients. In brief, non-proliferating (CFSEhi) and AP+ (CFSEdim) CD19+ CD27+ B cells from PBMCs of 5 natalizumab-treated female RRMS (NAT) patients were sorted following 7 days of autoproliferation. Transcriptome libraries were constructed from the same samples, except for one sample pair, which was excluded due to limited input material (5 donors as for Methylome, D1; D2, D3, D5, D6; samples from donor D4 unfortunately technically failed). SMARTer Total Stranded RNA-seq library construction with ribosomal depletion was performed and then sequenced on NovaSeq S4 lane.

  Dataset EGAD50000001270

• Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.

  Whole exome sequencing was performed from 108 Diffuse Large B Cell Lymphoma samples (99 FFPE tumor tissue derived DNA and 9 circulating tumor DNA) and corresponding germline DNA of 38 controls. A library containing whole exome regions was used to isolate the DNA for sequencing (SureSelect XT Human All Exon V6 (Agilent technologies)). Sequencing on a NovaSeq 6000 instrument (Illumina, paired end, 2x100, mean 566Gb per FlowCell) was performed.

  Dac EGAC50000000261

• Transcriptional profiles of Kleefstra syndrome (EHMT1 and EHMT2) and healthy fibroblasts

  This dataset contains FASTQ files from RNA sequencing (RNA-seq) of fibroblasts derived from a healthy donor (control), a patient with Kleefstra syndrome (KSP), and a patient carrying a pathogenic variant in EHMT2 (P2). Ribosomal RNA was removed using an RNase H–based depletion method, and strand-specific libraries were prepared for paired-end sequencing on the MGI DNBSEQ PE100 platform.

  Dataset EGAD50000002343

• WGS data from PASS-01 trial

  WGS data for pancreatic cancer samples (PASS-01 Trial; Knox et al., Journal of Clinical Oncology, 2025).  The dataset includes tumour and normal cram files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=127 tumour/normal pairs)

  Dataset EGAD50000002309

• WTS data from PASS-01 trial

  WTS data for pancreatic cancer samples (PASS-01 Trial; Knox et al., Journal of Clinical Oncology, 2025).  The dataset includes tumour bam files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=115 tumours)

  Dataset EGAD50000002308

• 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

• 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

• scRNAseq of endothelial cells from human iPSC-derived kidney organoids transplanted in the coelomic cavity of chicken embryos compared to untransplanted controls

  This dataset includes scRNA-seq fastq files and Seurat counts and metadata for 6 samples of endothelial cells enriched from hiPSC-derived kidney organoids cultured in vitro or transplanted in chicken embryos. Samples were obtained at 2 timepoints: d7+13 (1 day after transplantation) and day 7+20 (8 days after transplantation).

  Dataset EGAD50000001555

• Anti-MPO BCR sequences described in 'Anti-myeloperoxidase IgM B cells in anti-neutrophil cytoplasmic antibody-associated vasculitis'

  FASTA files from quality-checked Sanger Sequencing results from BCR-specific PCR products. B cells from 4 different MPO+ AAV patients were single cell sorted and processed to sequence the specific BCR, resulting in 51, 175, 12 and 3 heavy chain BCR sequences for AAV1, 2, 3, and 5 respectively. Sequence names indicate patient ID and isotype (IgG, IgM or IgA).

  Dataset EGAD50000001112

• Whole-exome sequencing of tumor samples

  Whole exome sequencing of DNA samples from tumor samples of patients in the Neo-Pembro trial. For each patient, up to four samples were sequenced; one tumor biopsy at baseline, one tumor biopsy after induction chemotherapy, a tumor sample from resection material at cytoreductive surgery, and a reference normal DNA sample isolated from whole blood. DNA was obtained from fresh-frozen samples where possible, or formalin-fixed paraffin-embedded when no fresh-frozen sample was available.

  Dataset EGAD50000001150

• Whole-transcriptome sequencing of tumor samples

  Whole transcriptome sequencing of RNA samples from tumor samples of patients in the Neo-Pembro trial. For each patient, up to three samples were sequenced; one tumor biopsy at baseline, one tumor biopsy after induction chemotherapy, and a tumor sample from resection material at cytoreductive surgery. RNA was obtained from fresh-frozen samples where possible, or formalin-fixed paraffin-embedded when no fresh-frozen sample was available.

  Dataset EGAD50000001151

• Clinical and demographics data from IMvigor210, IMvigor211, IMvigor130 and IMvigor010

  Clinical data include demographics (gender, race), specimen type (primary vs. metastatic), tract (upper vs. lower), liver metastasis status, PD-L1 IHC, tumor mutation burden, CD8 T cell infiltration status, neutrophil enrichment score, treatment arm, objective response rate, overall survival and progression free survival, and ctDNA status (IMvigor010 only) for 2803 patients across the four IMvigor trials.

  Dataset EGAD50000001101

• Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.

  Whole exome sequencing was performed from 108 Diffuse Large B Cell Lymphoma cases. A library containing whole exome regions was used to isolate the DNA for sequencing (SureSelect XT Human All Exon V6 (Agilent technologies)). Sequencing on a NovaSeq 6000 instrument (Illumina, paired end, 2x100, mean 566Gb per FlowCell) was performed.

  Dataset EGAD50000000546

• MCRI-WEHI GRREAT Ataxia Sequencing Cohort

  This study evaluated the effectiveness of long- and short-read sequencing as diagnostic tools for CA. We recruited 110 individuals (48 females, 62 males) with a clinical diagnosis of CA. Short-read genome sequencing (SR-GS) was performed to identify pathogenic RE and also non-RE variants in 356 genes associated with CA. Long-read adaptive sequencing (LR-AS) was performed to identify pathogenic RE in 67 genes.

  Dataset EGAD50000000815

• Epigenome-wide association study of asthma remission in whole blood and nasal epithelium

  Clinical remission (ClinR) was defined as the absence of asthma symptoms and medication for at least 12 months, and complete remission (ComR) was defined as ClinR with normal lung function and absence of airway hyperresponsiveness. We analyzed differential DNA methylation of ClinR and ComR comparing to persistent asthma (PersA) in whole blood samples (n=72) and nasal brushing samples (n=97) in a longitudinal cohort of well characterized asthma patients.

  Dataset EGAD00010002026

• Whole exome and RNA sequencing data from the OXIRI phase 1b clinical trial in Asian pancreatic ductal adenocarcinoma (PDAC) patients

  This dataset contains 8 samples, each of which has paired-end WXS fastq files for Tumour and Normal samples, as well as RNA-Seq fastq file.

  Dataset EGAD00001008632

• WGS data subfolder HF3J5CCXY from multifocal ileal NETs study

  This dataset includes linked-read whole-genome sequencing data (subfolder HF3J5CCXY) for multifocal ileal tumor samples from one patient. Samples were sequenced using the 10x Genomics linked-read whole-genome sequencing (WGS) approach.

  Dataset EGAD00001008493

• Unifying recovery dynamics in heterogeneous diseases exemplified by COVID-19

  To model recovery dynamics, using severe COVID-19 as the example, we align heterogeneous recovery trajectories via a novel computational scheme applied to longitudinally sampled blood transcriptomes. We thus generate pseudotime trajectories, which we then link to cellular and molecular mechanisms based on cell deconvolution analysis and molecular pathway prediction, thus presenting a unique framework for studying recovery processes over time.

  Dataset EGAD00001008331

• Genomic abnormalities of TP53 define distinct risk groups of paediatric B-cell non-Hodgkin lymphoma

  Whole exome sequencing data from 90 diagnostic lymphoma samples run and published as part of the Leukemia manuscript. 133 total exomes were sequenced including tumour and normal controls. Copy number array data was also generated for 95 patients.

  Dataset EGAD00001008162

• The University of Hong Kong Colon Cancer Ganciclovir Study WGS Data

  Human clonal intestinal organoids were treated with 1µM MMF (Roche), 20 μM GCV (Hainan Poly Pharm Co Ltd), or in combinations (1 µM MMF + 20 μM GCV or 1 µM MMF + 40 μM GCV) continuously for 4-6 weeks. DNA was extracted after drug treatment. WGS was performed with 150 bp PE sequencing at 30X using an Illumina Novaseq sequencer.

  Dataset EGAD00001009667

• BCG Molecular Subtyping

  Dataset for the paper: Non-muscle Invasive Bladder Cancer Molecular Subtypes Predict Differential Response to Intravesical Bacillus Calmette-Guérin

  Dataset EGAD00001010065

• WES raw data set for the study "Genomic profiling of localized (lFL) and systemic follicular lymphoma (sFL) reveals novel insights into FL pathogenesis"

  221 patient samples including 164 initial tumor (TI) samples (53/164 fresh frozen TI samples, and 111/164 formalin-fixed paraffin-embedded (FFPE) TI samples), 22 paired matched normal samples, and 35 unpaired normal samples from healthy donors; FASTQ file format, Agilent SureSelect Human All Exon V6 Kit (Agilent Technologies, Inc., Santa Clara, California, USA)

  Dataset EGAD00001011369

• V2 Colorectal panel test

  Targeted gene screen of cell line tumour samples for testing the new V2 Colorectal gene panel.

  Dataset EGAD00001003253

• Genomic Profiling of Advanced Pancreatic Cancer to inform therapy - RNA-Seq unmapped reads

  Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer - Early Results from the COMPASS Trial - RNA-Seq unmapped reads

  Dataset EGAD00001003582

• Low-coverage Whole Genome Sequencing, Colorectal adenomas, NKI-AvL TGO series Stool-Proteomics

  For this tissue dataset, we applied low-pass whole genome sequencing to 98 non-advanced and advanced adenomas. As small number of lesions was sequenced multiple times, this dataset consists of 103 fastq files. These adenomas were classified as lesions with low-risk or high-risk of progression, according to the presence of specific DNA copy number changes (Carvalho et al, CancerPrevRes, 2018).

  Dataset EGAD00001004075

• Clonal cultures of T memory cells

  Sequence data (bam files) of two RRBS samples for paper "A comprehensive analysis of 195 DNA methylomes reveals shared and cell specific features of partially methylated domains". Short Description: CD4+ T memory cells (CD3+ CD4+ CD45RA- CD45RO+ CD25-) from donors were sorted by flow-cytometry either as a bulk culture ('ex vivo' sample) or in a single-cell format into 96 well-plates ('clone' sample) in the presence of a TCR stimulus.

  Dataset EGAD00001004303

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - 100_all_samples

  All samples from the "100" project

  Dataset EGAD00001001457

• LINE luminal breast cancer Neoadjuvant Chemotherapy Study (2019-08-28)

  A targeted gene screen of 365 known cancer genes in luminal breast cancer samples pre-chemotherapy and at resection post-chemotherapy to evalaute clonal expansion of chemotherapy cancer cells. . This dataset contains all the data available for this study on 2019-08-28.

  Dataset EGAD00001005297

• Whole exome sequencing of advanced gastric cancer

  To define the cellular characteristics of malignant ascites of advanced gastric cancer patients and search for therapeutic strategies, we obtained 5 malignant ascites and 1 cerebrospinal fluid from five patients with gastric cancer. We analyzed single-cell RNA-seq data of 180 cells from 4 malignant ascites and 1 cerebrospinal fluid metastasis using Fluidigm® C1™ System. Whole exome sequencing data was also generated from blood or tumor tissue.

  Dataset EGAD00001005740

• Analysis for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (scRNA analysis)

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. Single cell metadata and analysis 38 Barrett's and normals

  Dataset EGAD00001005455

• Omics data of advanced bladder cancer

  To identify the therapeutic targets in a treatment-refractory cancer patient, we performed single-cell RNA sequencing for 3,115 cells from primary bladder cancer (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). Matched time-series bulk tumor tissues were also sequenced using whole exome target probe (WES) and whole transcriptome target probe (WTS).

  Dataset EGAD00001005978

• Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls

  We created three technical replicates of cell-free DNA from AML patient plasma to assess batch effects and utility of spike-in controls for the cfMeDIP-seq method. Each set of samples were given to three different technicians with slightly different protocols. Details can be found in Wilson et al. "Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls".

  Dataset EGAD00001006986

• Genetics causes of male infertility in 185 patient-parent trios from Netherlands and UK

  The dataset is composed by the raw and processed sequencing data generated from 185 Patients affected by azoospermia or severe oligozoospermia recruited from the Netherlands and the UK.

  Dataset EGAD00001007862

• cfDNA sWGS BAM — Healthy donors

  Paired-end shallow whole-genome sequencing (sWGS) of plasma cfDNA from healthy donors recruited at EFS Montpellier (France). Libraries: DSP (NEBNext Ultra II) and/or SSP (IDT/Swift Accel-NGS 1S Plus). Sequencing by IntegraGen (France, 2022–2024). Reads aligned to GRCh38 (hg38 canonical) with BWA-MEM; BAMs coordinate-sorted and indexed; submission contains primary mapped reads only (unmapped/secondary/supplementary/duplicates removed; typical filter “-F 3332”, MAPQ threshold as noted in analysis records). Each BAM/BAI pair is linked to its Sample and Experiment. Data Use: controlled access.

  Dataset EGAD50000001880

• Whole-genome and single-cell sequencing of lethal metastatic castration resistant prostate cancer

  Contains a total of 9 patients with whole-genome sequencing of 30 tumours or germline samples, 10X single-cell multiome RNA-seq + ATAC-seq of 24 tumours, 10X 5' single-cell RNA-seq of 10 tumours, and snPATHO-seq of 2 primary tumours. All single-cell experiments have matched whole-genome sequencing. When matched tumour (and germline) whole-genome sequencing is missing, it can be found under EGAS00001006598.

  Dataset EGAD50000001869

• De novo modeling of chromoplectic Ewing sarcoma tumors from patient-derived mesenchymal stem cells

  Ewing sarcoma is characterized by pathognomonic translocations fusing most frequently EWSR1 with FLI1 (EF1). In addition, Ewing sarcoma can also display alterations in STAG2, TP53 and CDKN2A (SPC). Starting from Ewing sarcoma derived human mesenchymal stem cells (MSCpat), we recapitulated this translocation and SPC alterations using a CRISPR/cas9 approach and generated a bona fide Ewing sarcoma model (EWIma1) displaying transcriptomic (RNA-seq) and epigenetic (ChIP-seq) hallmarks of EwS.

  Dataset EGAD50000001673

• Multiomic characterization of clonotypic B cells

  DNA was purified using AMPure XP magnetic beads (Beckman Coulter [BC] Life Sciences, Indianapolis, IN) and its quality was evaluated in an Agilent 4200 Tapestation using the Genomic DNA ScreenTape system (Agilent, Santa Clara, CA). DNA was quantified using the Qubit System (Invitrogen). Extracted DNA from AL patients was fragmented to 200bp by a Covaris S220 ultrasonicator (Covaris, Woburn, MA) and used to generate and capture libraries following the manufacturer’s indications from Twist Bioscience’s Human Core Exome Enrichment Kit (Twist Bioscience). Extracted DNA from MM patients and HA was fragmented to an average size of 225 bp using a Covaris S220 ultrasonicator (Covaris, Woburn, MA) and subjected to DNA library construction using Chromium Genome Reagent Kit V2 for Exome Assays (10X Genomics). Target enrichment was performed with SureSelectXT Human All Exon V6 Capture Library (Agilent) or SureSelectXT2 Human All Exon V5+UTRs (Agilent), and sequence targets were captured and amplified in accordance with the manufacturer’s protocol. Final libraries were combined with standard Illumina sequencing primers and paired-end sequenced (150bp) on a HiSeq X platform (Illumina, CA) or in a NovaSeq 6000 (Illumina).

  Dataset EGAD50000002162

• Spatial and temporal intra-tumoural heterogeneity in advanced High-Grade Serous Ovarian Cancer: implications for surgical and clinical outcomes

  Limited evidence exists on the extent and impact of spatial and temporal heterogeneity of high grade serous ovarian cancer (HGSOC) on tumour evolution and patients surgical and clinical outcome. We investigated this through systematic mapping of multi-site tumours at initial presentation and matched relapse from 49 chemo-naïve HGSOC patients with high tumour load, operated upfront. Our data provides a unique insight into the tumour evolution and metastatic pathways of HGSOC across time and space, how this complexity relates to surgical and clinical outcome and its consequences on clinical decision-making.

  Study EGAS00001007164

• DNA Replication Speed controls Epigenome Integrity and T Cell Fate

  Epigenetic mechanisms maintain cellular identities by enforcing stable, cell type-specific transcriptional programs while also allowing regulated plasticity for adaptations to environmental cues like differentiation signals. Dysregulation of this dual capacity has been linked to cancer and chronic inflammation, with the regulatory mechanisms remaining poorly understood. Here, we identify DNA replication speed as a physiological regulator controlling epigenome stability and plasticity. Using T-lymphocytes as a model, we demonstrate that fast DNA replication speed impaired epigenome stability, causing DNA methylation maintenance errors at cell type-specific enhancers and heterochromatin, ultimately leading to compromised cell function. However, accelerated DNA replication speed supported epigenome plasticity during differentiation, promoting successful cell-type transitions

  Study EGAS50000001273

• Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

  Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de-novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondaryrearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.

  Study EGAS00001000659

• Identification and functional characterisation of a rare MTTP variant underlying familial non-alcoholic fatty liver disease

  We identified a rare causal variant in MTTP, c.1691T>C p.I564T (rs745447480) encoding microsomal triglyceride transfer protein (MTP) causing progressive non-alcoholic fatty liver disease with cirrhosis and hepatocellular carcinoma unrelated to metabolic syndrome, without manifestations of abetalipoproteinemia, in a four generation family with South Asian ancestry. Variant-expressing hepatocyte-like-cells (HLCs) derived from human induced pluripotent stem cells generated from homozygous donor skin fibroblasts had lower lipoprotein ApoB secretion, compared to wild type cells. Cytoplasmic triglyceride accumulation in HLCs triggered endoplasmic reticulum stress, secretion of pro-inflammatory mediators, production of reactive oxygen species, delineating the progression of disease associated with homozygosity for MTTP p.I564T

  Study EGAS00001005254

• CRUK-ICGC Prostate DNA Methylation Sequencing Dataset (Prostatectomy Batches 1-6)

  This dataset includes Illumina EPIC Capture Sequencing Data of 376 samples from 188 men with prostate cancer. Samples were taken from primary tissue obtained at prostatectomy, with matched pathologically assessed non-cancer control material. This DNA methylation data includes donors and samples included in previously published WGS datasets (from CRUK-ICGC batches 1 to 3 [EGAD00001001116] and batches 4 to 6 [EGAD00001003225]; including the majority of donors used in Wedge et al, Nature Genetics 2018 [PMID: 29662167]). The targeted DNA methylation sequencing data in this EGA dataset were generated using the Illumina TruSeq methyl capture method (EPICseq), covering over 3.3 million CpGs in the human genome, representing a total targeted hybridisation capture panel of 107Mbp. According to the EPICseq protocol, DNA samples extracted from prostatectomy tissue samples were enriched for target regions using hybridisation capture, prior to bisulfite conversion, amplification and sequencing in pools of 12 samples (150 single end reads over two Illumina HiSeq4000 lanes). This approach generated DNA methylation profiles from prostate cancer and control samples at base-pair resolution across millions of CpGs in the human genome.

  Dataset EGAD00001010184

• Comprehensive Omics Analysis of Pediatric Solid Tumors and Establishment of a Repository for Related Biologic Studies (10C0086)

  This study (10-C-0086) collected and analyzed tumor and circulating tumor omics of pediatric and young adult patients with relapsed rhabdomyosarcoma who were co-enrolled in and receiving treatment on the interventional study 17-C-0049. We sought to describe the summary genomic findings of tumors, and report on the detection of circulating tumor DNA (ctDNA) in serial samples. Tumor tissue and blood were collected and analyzed. Tumor samples were subjected to whole exome and/or whole genome sequencing paired with RNA-Seq. Cell free DNA (cfDNA) was extracted from serially collected blood samples and sequenced. Fusion status, mutations, and IGF1R and YES1 expression from tumor samples revealed the presence of a PAX3 fusion in most samples, a number of common mutations, and universal but heterogeneous expression of IGF-1R and YES1. ctDNA was detected above the 3% threshold in a majority of patients and analysis of cfDNA demonstrated an ability to monitor tumor clonal evolution.

  Study phs003243

• Multi-organ landscape of therapy-resistant melanoma

  Metastasis and failure of present-day therapies represent the most common causes of mortality in patients with cutaneous melanoma. To identify the underlying genetic and transcriptomic landscapes, here we analyzed multi-organ metastases and tumor-adjacent tissues from eleven rapid autopsies after treatment with MAPK inhibitor (MAPKi) and/or immune checkpoint blockade (ICB) and death due to acquired resistance. Either treatment elicits shared genetic alterations that suggest immune-evasive, cross-therapy resistance mechanisms. Large, non-clustered deletions, inversions, and inter-chromosomal translocations dominate rearrangements. Using 345 therapy-naïve TCGA melanoma and 131 patient-matched melanoma pre-and-post acquired resistance to only either treatment, we performed cross-cohort analyses to identify MAPKi and ICB as respective contributors to gene amplifications and deletions enriched in autopsy versus therapy-naïve tumors. Private/late mutations and structural variants display shifted mutational and rearrangement signatures, with MAPKi specifically selecting for signatures of defective homologous-recombination, mismatch, and base-excision repair. Transcriptomic signatures and cross-talks with tumor-adjacent macroenvironments nominate organ-specific adaptive pathways. An immune-desert, CD8+-macrophage-biased archetype, T-cell exhaustion, and type-2 immunity characterize the immune contexture. This multi-organ analysis of lethal, therapy-resistant melanoma presents preliminary insights with potential to improve therapeutic strategies.

  Study EGAS00001006644

• Pooled scRNA-seq of iPSC-derived neural stem cells from ADHD and control individuals

  This dataset comprises paired-end FASTQ files from single-cell RNA sequencing (scRNA-seq) of neural stem cells (NSCs) derived from induced pluripotent stem cells (iPSCs). The iPSCs were reprogrammed from somatic cells (keratinocytes, PBMCs, or lymphoblastoid cell lines) collected from individuals diagnosed with attention-deficit hyperactivity disorder (ADHD) and age-matched healthy controls (ages 6–18 years). Reprogramming was carried out using the non-integrative Sendai virus system (CytoTune-iPS 2.0, Thermo Fisher Scientific), introducing OCT3/4, SOX2, KLF4, and cMYC. iPSCs were cultured in Essential 8 medium on vitronectin and underwent rigorous quality control including immunocytochemistry, qRT-PCR, mycoplasma testing, and SNP genotyping (Illumina Global Screening Array). NSCs were generated using a standardized neural induction protocol and validated via qRT-PCR and immunostaining for markers including PAX6, SOX2, NESTIN, TUJ1, and FOXG1. Two independent scRNA-seq multiplexed experiments were performed: Experiment 1 (ADHD: n = 7; Control: n = 6) and Experiment 2 (ADHD: n = 9; Control: n = 7). Samples were pooled and demultiplexed using the Ensemblex algorithm, incorporating prior genotype data. After quality control filtering (>500 unique RNA molecules per cell), 30,433 single-cell transcriptomes were retained. Differential gene expression analysis was conducted to identify transcriptional signatures associated with ADHD compared to controls.

  Study EGAS00001008169