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• RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial.

  DAC for RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial.

  Dac EGAC50000000627

• Germline RUNX1 Variation and Predisposition to Childhood Acute Lymphoblastic

  Somatic mutations of RUNX1, which encodes the myeloid and lymphoid transcriptional factor RUNX1, are common in both B- and T- acute lymphoid leukemia (ALL) and are associated with poor prognosis of T-ALL. However, there has been no comprehensive investigation of the pattern or prevalence of RUNX1 germline mutation in both B- and T-ALL. Here we report germline RUNX1 variants in 1.23% of B-ALL and 2.11% of T-ALL, identifying 31 unique variants in 62 B-ALL and 18 unique variants in 26 T-ALL children. The majority of frameshift and nonsense variants affected RUNX1 function in transcriptional regulation, hematopoiesis, and cellular proliferation. We identified JAK3 as the most frequent somatic mutation in T-ALL with RUNX1 variants. These results not only identify RUNX1 as a leukemia predisposition gene but also further underline the importance of germline genetic variants to the development of ALL

  Dataset EGAD00001007793

• RNA-seq of high grade serous ovarian tumours

  Somatic RNA for 40 samples matched to the WGS was extracted using the Qiagen Qiasymphony RNA protcol (cat no 931636). The tissue was initially homogenised using a Qiagen Bioruptor, followed by the manufacturers recommended protocol (including DNase digestion). The resulting RNA the underwent quality control as follows: firstly, A260 and A280nm were measured on a Denovix DS-11 Fx to qualitatively illustrate A260/280nm and A260/230nm ratios as measures of RNA purity. A260/280 had to be 2.0 and A260/230 had to be 2.0-2.2. Then RNA was quantified using LifeTechnologies Qubit RNA BR kit (cat no Q10210). RNAseq was carried out by the Edinburgh Clinical Research Facility on an Illumina NExtSeq500. Total RNA samples were assessed on the Agilent Bioanalyser (Agilent Technologies, #G2939AA) with the RNA 6000 Nano Kit (#5067-1512) for quality and integrity of total RNA, and then quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, #Q32866) and the Qubit RNA HS assay kit (#Q32855). Libraries were prepared from total-RNA sample using the NEBNext Ultra 2 Directional RNA library prep kit for Illumina (#E7760S) with the NEBNext rRNA Depletion kit (#E6310) according to the provided protocol. 400ng of totalRNA was then added to the ribosomal RNA (rRNA) depletion reaction using the NEBNext rRNA depletion kit (Human/mouse/rat) (#E6310). This step uses specific probes that bind to the rRNA in order to cleave it. rRNA-depleted RNA was then DNase treated and purified using Agencourt RNAClean XP beads (Beckman Coulter Inc, #66514). RNA was then fragmented using random primers before undergoing first strand and second strand synthesis to create cDNA. cDNA was end repaired before ligation of sequencing adapters, and libraries were enriched by PCR using the NEBNext Multiplex oligos for Illumina set 1 and 2 (#E7500). Final libraries had an average peak size of 271bp. Libraries were quantified by fluorometry using the Qubit dsDNA HS assay and assessed for quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626). Sequencing was performed using the NextSeq 500/550 High-Output v2 (150 cycle) Kit (# FC- 404-2002) on the NextSeq 550 platform (Illumina Inc, #SY-415-1002). Libraries were combined in an equimolar pool based on the library quantification results and run across 5 High-Output Flow Cell v2.5.

  Dataset EGAD00001009048

• RNA-seq of high grade serous ovarian tumours

  Somatic RNA for 37 samples was extracted using the Qiagen Qiasymphony RNA protcol (cat no 931636). The tissue was initially homogenised using a Qiagen Bioruptor, followed by the manufacturers recommended protocol (including DNase digestion). The resulting RNA the underwent quality control as follows: firstly, A260 and A280nm were measured on a Denovix DS-11 Fx to qualitatively illustrate A260/280nm and A260/230nm ratios as measures of RNA purity. A260/280 had to be 2.0 and A260/230 had to be 2.0-2.2. Then RNA was quantified using LifeTechnologies Qubit RNA BR kit (cat no Q10210). RNAseq was carried out by the Edinburgh Clinical Research Facility on an Illumina NExtSeq500. Total RNA samples were assessed on the Agilent Bioanalyser (Agilent Technologies, #G2939AA) with the RNA 6000 Nano Kit (#5067-1512) for quality and integrity of total RNA, and then quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, #Q32866) and the Qubit RNA HS assay kit (#Q32855). Libraries were prepared from total-RNA sample using the NEBNext Ultra 2 Directional RNA library prep kit for Illumina (#E7760S) with the NEBNext rRNA Depletion kit (#E6310) according to the provided protocol. 400ng of totalRNA was then added to the ribosomal RNA (rRNA) depletion reaction using the NEBNext rRNA depletion kit (Human/mouse/rat) (#E6310). This step uses specific probes that bind to the rRNA in order to cleave it. rRNA-depleted RNA was then DNase treated and purified using Agencourt RNAClean XP beads (Beckman Coulter Inc, #66514). RNA was then fragmented using random primers before undergoing first strand and second strand synthesis to create cDNA. cDNA was end repaired before ligation of sequencing adapters, and libraries were enriched by PCR using the NEBNext Multiplex oligos for Illumina set 1 and 2 (#E7500). Final libraries had an average peak size of 271bp. Libraries were quantified by fluorometry using the Qubit dsDNA HS assay and assessed for quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626). Sequencing was performed using the NextSeq 500/550 High-Output v2 (150 cycle) Kit (# FC- 404-2002) on the NextSeq 550 platform (Illumina Inc, #SY-415-1002). Libraries were combined in an equimolar pool based on the library quantification results and run across 5 High-Output Flow Cell v2.5.

  Dataset EGAD00001010139

• Dataset of BAM files of three trio members

  This dataset contains whole genome sequencing data, based in BAM files of three trio members. These BAM files contain information of chromsomes 21, X, Y and mitochondrial.

  Dataset EGAD00001008095

• Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer

  Gene expression profiles of single cells from 26 chemo-naïve and IDS tumor tissue and ascites samples from 17 HGSC patients

  Study EGAS50000000607

• dataset1

  Contains 14 control samples and 26 case samples.

  Dataset EGAD00001008576

• BLUEPRINT release August 2015, ChIP-Seq for CD8-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 5 CD8-positive, alpha-beta T cell sample(s). 26 run(s), 26 experiment(s), 26 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001513

• MeDALL epigenetics study

  MeDALL- (Mechanisms of the Development of ALLergy) is a collaborative project supported by the European Union under the Health Cooperation Work Programme of the 7th Framework programme (grant agreement number 261357).MeDALL epigenetics study includes illumina 450k methylation measurements from 4 cohorts: Infancia y Medio Ambiente (INMA), Etudes des Déterminants pré et postnatals précoces du développement et de la santé de l’ENfant (EDEN), Children’s Allergy Environment Stockholm Epidemiology study(BAMSE), and Prevention and Incidence of Asthma and Mite Allergy (PIAMA)

  Study EGAS00001002169

• C9orf72 region reads of 3001 samples

  This dataset includes cram files from 3,001 samples. These cram files include all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion. Additionally, these cram files also contain reads that are aligned to any of 29 pre-determined off target locations where the aligners are known to mis-align reads associated with this repeat expansion. These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer and aligned using the Isaac aligner.

  Dataset EGAD00001004834

• Sequencing files for "Transcriptional Mechanisms of Resistance to Anti-PD-1 Therapy"

  Files from whole exome sequencing of 26 tumors and two matched normals from one melanoma patient. The 26 tumors include the untreated primary, cutaneous metastases and distant metastases to internal organs.

  Dataset EGAD00001003200

• Non-coding mutations reveal cancer driver cistromes in luminal breast cancer

  A dataset of ER+PR+ breast tumor samples that were analyzed in order to identify mutation enrichment in cis-regulatory elements and cistrome. The repository includes sequencing data from 88 patients. 26/88 were sequenced using ATAC-seq

  Dataset EGAD00001007650

• GenomeDenmark Phase 2 - variants called on chrY for 62 males.

  Variants on the Y chromosome for 62 danish males in VCF format from the GenomeDenmark Phase 2 cohort. Variants were called using reference based approaches such as the haplotype-caller module from GATK and using alignment of denovo assemblies to the reference using ASMvar.

  Dataset EGAD00001003186

• High-throughput transcriptome data of paediatric ETV6-RUNX1 acute lymphoblastic leukemia

  High-throughput transcriptome sequencing data from paediatric (<18-y) ETV6-RUNX1 fusion positive acute lymphoblastic leukemias. Dataset includes fastq and BAM files from diagnostic samples of 33 patients.

  Dataset EGAD00001010164

• Phenotype information

  This study explores the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft (PDTX) model. Blood plasma samples (n=171) derived from a DLBCL PDTX model in-cluding 27 humanized (HIS) PDTX, 8 HIS non-PDTX and 21 non-HIS PDTX non-obese diabetic (NOD)-scid IL2Rgnull (NSG) mice were collected during humanization, xenografting, treatment, and sacrifice. The mice were treated with either rituximab, cyclophosphamide, doxorubicin, vincris-tine, and prednisone (R-CHOP), CD20-targeted human IFNα2-based AcTaferon combined with CHOP (huCD20-Fc-AFN-CHOP), or phosphate-buffered saline (PBS). RNA was extracted using the miRNeasy serum/plasma kit and sequenced on the NovaSeq 6000 platform using the using the SMARTer Stranded Total RNA-Seq Kit v3.

  Dataset EGAD50000000806

• Long-read data (PacBio)

  The goal of this project was to perform long-read RNA sequencing (LR-seq, PacBio) in combination with short-read RNA-seq for systematic characterization of the isoform diversity in primary breast tumor samples. We sequenced the full-length transcriptomes of 26 breast tumors and 4 normal breast samples.

  Dataset EGAD00001006597

• Sahel Data Access Committee

  Genome-wide genotype array data of Fulani populations presented in Fortes-Lima et al. 2025. Citation: Population History and Admixture of the Fulani People from the Sahel. Cesar A. Fortes-Lima, Mame Y. Diallo, Václav Janoušek, Viktor Černý, and Carina M. Schlebusch. American Journal of Human Genetics 112(2), February 6, 2025. doi: https://doi.org/10.1016/j.ajhg.2024.12.015

  Dac EGAC50000000290

• Drug Perturbation of Primary Lymphoma Patient Samples and RNA Sequencing

  This submission contains 3'-end-based shallow-depth RNA sequencing data from 108 patients with chronic lymphocytic leukemia and 8 patients with lymphoma. Each primary patient sample was treated in vitro with DMSO as a control and with up to ten small-molecule drugs (ibrutinib, duvelisib, everolimus, trametinib, nutlin-3a, I-BET762, MK2206, selinexor, compound 26, and a combination of ibrutinib and compound 26). The samples were sequenced after 48 hours. The total data set consists of 1476 RNA sequencing samples from 6 batches (pilot, batch 1, batch 1 replicate, batch 2, batch 3, batch 4).

  Study EGAS50000001500

• Bladder Cancer Organoids as a Functional System to Model Different Disease Stages and Therapy Response

  The study 'Bladder Cancer Organoids as a Functional System to Model Different Disease Stages and Therapy Response' reports the genomic characterization at the single allele level upon Whole Exome Sequencing of Bladder Cancer (BLCa) Patient Tumor (PT) samples obtained from 18 patients and corresponding Patient Derived Organoids (PDOs), implementing the SPICE pipeline (Ciani Y et al). Our cohort included 21 PTs and 22 PDOs. In this study, we generated a unique biobank resource of BLCa organoids that encompasses a broad spectrum of disease stages. We demonstrated that PDOs retain cancer heterogeneity and mutational burden. Furthermore, we observed that BLCa PDO can have different morphologies which may reflect tumor-specific features. Indeed, a solid morphology may be associated with more advanced tumors, as supported by the high PDO genomic burden and high primary tumor stage. Moreover, with our drug screening pipeline, we demonstrated the clinical relevance and feasibility of using a BLCa PDO-based drug assay for comparing the standard of care (SOC) drugs with compounds not currently in use for BLCa. Response to SOC was highly heterogeneous with approximately 50% of non-muscle invasive bladder cancer and 33% of muscle invasive bladder cancer PDOs showing no or minimal response. The most effective targeted therapy was lapatinib. We used an integrative analysis of drug response profiles with matched PDO genomic analysis to determine enrichment thresholds for candidate markers of therapy resistance and sensitivity. Importantly, by assessing the clinical history of longitudinally sampled cases, the clonal evolution of the disease could be determined and matched with PDO drug response profiles.

  Study phs003149

• Lymphoma_primary_patient_drug_perturbed_RNASeq_samples

  3'-end low-depth RNA sequencing data from 108 patients with chronic lymphocytic leukemia and 8 patients with lymphoma. Each primary patient sample was treated in vitro with DMSO as a control and with up to ten small-molecule inhibitors (ibrutinib, duvelisib, everolimus, trametinib, nutlin-3a, I-BET-762, MK2206, selinexor, compound 26, and a combination of ibrutinib and compound 26). Sequencing was performed on the Illumina HiSeq4000. The dataset contains FASTQ files.

  Dac EGAC50000000578

• scMultiome (snRNA + snATAC) data of 26 regionally sampled GBM tissue from 6 patients

  This dataset contains snRNA-seq data of 26 regionally sampled GBM tissue (peritumoral region, tumor edge, and tumor core). Regionally sampled GBM patient tissue was dissociated and nuclei were processed unsorted or by sorting with 7AAD to remove debris and dead cells. Single-nuclei suspension was prepared following the nuclei isolation protocol Single Cell Multiome ATAC + Gene Expression Sequencing protocol using Chromium Nuclei Isolation Kit. Single-nuclei suspension was prepared following the nuclei isolation protocol Single Cell Multiome ATAC + Gene Expression Sequencing protocol using Chromium Nuclei Isolation Kit, nuclei were barcoded and RNA and ATAC libraries were constructed, allowing for simultaneous capture of transcriptome and epigenome from the same cells.

  Dataset EGAD50000001838

• Exome-sequencing of human B cell lymphoma cell lines

  26 cell lines derived from human Diffuse Large B Cell lymphomas (DLBCL) or Burkit Lymphomas (BL) were subjected to whole exome sequencing. Exome capture was carried out using the SeqCap EZ Exome Library 2.0 kit (Roche/Nimblegen) and 100 bp single-read sequencing was performed on a HiSeq2500 (Illumina). 82% of the coding region was covered at least 30x.

  Dataset EGAD00001002262

• INSPIRE - Investigator-initiated Phase 2 Study of Pembrolizumab Immunological Response in Metastatic Solid Tumors

  Whole exome and RNA sequencing source data for: Clouthier, D.L., Lien, S.C., Yang, S.Y.C. et al. An interim report on the investigator-initiated phase 2 study of pembrolizumab immunological response evaluation (INSPIRE). j. immunotherapy cancer 7, 72 (2019). https://doi.org/10.1186/s40425-019-0541-0 Bratman S*, Yang SYC*, Iafolla MAJ, Liu Z, Hansen AR, Bedard P, Lheureux S, Spreafico A, Razak AA, Shchegrova S, Louie M, Billings P, Zimmerman B, Sethi H, Aleshi A, Torti D, Marsh K, Eagles J, Cirlan I, Hanna Y, Clouthier D, Lien SC, Ohashi PS, Xu W, Siu LL, Pugh TJ. Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab. Nature Cancer. 2020:1:873-881. https://doi.org/10.1038/s43018- 020-0096-5. Yang SYC, Lien SC, Wang BX, Clouthier DL, Hanna Y, Cirlan I, Zhu K, Bruce JP, El Ghamrasni S, Iafallo MAJ, Oliva M, Hansen AR, Spreafico A, Bedard PL, Lheureux S, Razak A, Speers V, Berman HK, Aleshin A, Haibe-Kains B, Brooks DG, McGaha TL, Butler MO, Bratman SV, Ohashi PS, Siu LL, and Pugh TJ. Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity. Nature Comm 2021:12, 5137. https://doi.org/10.1038/s41467-021-25432-7

  Study EGAS00001003280

• WES in muscle-invasive bladder cancer (MIBC) treated with durvalumab plus olaparib in the neoadjuvant setting: NEODURVARIB trial

  This submission contains the metadata derived from the whole exome sequencing of 70 samples from 26 patients who developed advanced urothelial carcinomas. The patients were enrolled in the Neodurvarib clinical trial, which compares the molecular profiles at diagnosis and after neoadjuvant treatment with Durvalumab and Olaparib. In this regard, the analyzed samples include: normal tissue and tumoral tissue obtained from the transurethral resection of the bladder (TURBT, a procedure performed prior to neoadjuvant therapy) from the 26 patients (52 samples), as well as tissue obtained from the radical cystectomy (a procedure performed after treatment with the aforementioned drugs; 18 samples).

  Study EGAS50000000791

• Whole Exome Sequencing of gliomas

  Dataset EGAD00001001614