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• Assessing gene expression profiling from FFPE Patient Samples: A Comparison of Two Library Preparation Approaches and Recommendations

  Next-Generation Sequencing (NGS) has transformed cancer research and clinical practice, with Whole Exome Sequencing (WES) driving advances in mutational profiling and personalized oncology. Yet, transcriptomic signatures remain essential for understanding disease mechanisms, including therapy resistance pathways. RNA sequencing (RNA-seq), however, faces unique challenges when dealing with low-input or degraded RNA, as often found in archival formalin-fixed paraffin-embedded (FFPE) tissues. Although previous studies have compared library preparation protocols, rapidly evolving technologies call for updated evaluations. Here, we present a direct comparison of two FFPE-compatible stranded RNA-seq library preparation kits: TaKaRa™ SMARTer® Stranded Total RNA-Seq Kit v2 (Kit A) and Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Kit B). Both kits generated high-quality RNA-seq data, yet important differences emerged. Notably, Kit A achieved comparable gene expression quantification to Kit B while requiring 20-fold less RNA input, a crucial advantage for limited samples, albeit with increased sequencing depth. We critically discuss these results in relation to RNA availability, technical performance, cost-effectiveness, processing time, and automation potential, offering practical guidance for selecting optimal RNA-seq strategies in clinical and translational research settings

  Study EGAS50000001066

• Single cell RNA sequencing of lung adenocarcinoma.

  We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes.

  Study EGAS00001003681

• Roifman DAC

  This Data Access Committee will oversee all requests for data submitted by Dr. Chaim Roifman at the Hospital for Sick Children in Toronto, Canada. Requests should be directed by email to chaim.roifman@sickkids.ca.

  Dac EGAC50000000396

• Thymic epithelial transplantation for complete DiGeorge syndrome Spatial (2025-07-28)

  Spatial transcriptomics study of thymic transplant biopsies . This dataset contains all the data available for this study on 2025-07-28.

  Dataset EGAD00001015659

• RNASeq files for Mullighan ECOG2993 data

  RNASeq files for paper titled "Molecular classification improves risk assessment in adult B-lineage ALL: Patients on the international UKALLXII-ECOG2993 trial."

  Dataset EGAD00001006380

• Bulk and single-cell AML RNA-seq post ex vivo culture

  Bulk and single-cell RNA-seq performed on primary AML blasts cultured ex vivo for 3 days in standard or niche-like conditions.

  Study EGAS00001006265

• DAC anti-MPO BCR sequences

  DAC for the requests of access to data of anti-MPO BCR sequences in the EGA repository,

  Dac EGAC50000000446

• NGS WGS Data - Unic TDP

  WGS data from the Unicorn-PASS cohort for the Tandem Duplicator Phenotype paper

  Dataset EGAD50000001567

• March 2018 cumulative data release for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2018 cumulative data release (bams,fastqs) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium

  Dataset EGAD00001003963

• Use of Deep Sequencing to Dectect Clonal Mutations In Sun Exposed Skin Epidermis

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Dataset EGAD00001001090

• Data of the Institute of Pathology, University Medical Center Freiburg, Germany

  DAC for proteomics data deposited in EGA by the proteomics laboratory of the Institute of Pathology, University Medical Center Freiburg, Germany

  Dac EGAC50000000048

• Sensitive gene analysis of hereditary cardiovascular disease

  This research aims to identify disease sensitive genes and their gene variants by genome analysis for hereditary cardiovascular diseases.

  Study JGAS000295

• Whole genome sequencing of AML samples at presentation, remission, and relapse

  Whole genome sequencing of AML blood or bone marrow at presentation and remission for 5 patients. Relapse samples are included for 2 patients, totaling 12 WGS BAM files.

  Dataset EGAD00001005120

• Single nucleus and spatial transcriptomic characterization of prostate cancer versus normal controls

  10x Genomics Visium and Chromium platforms were used for spatial and single-nuclei RNA-sequencing, respectively. Cohort consisted of 8 prostate cancer patients (8 prostate cancer + 8 paired non-malignant control samples, fresh-frozen)

  Study EGAS50000001143

• Transcriptional and epigenetic profiling of bone marrow blood progenitors across age

  Bone marrow from donors without known malignancy was isolated and CD34-enriched, FACS-purified to further enrich for CD34+CD38- primitive cells, and then profiled by single-cell 10X genomics chromium Multiome (RNA+ATAC).

  Study EGAS50000001623

• Genomic and clinical data from IMmotion010, a phase 3 randomised clinical trial testing adjuvant atezolizumab versus placebo for patients with renal cell carcinoma at increased risk of recurrence following resection

  778 patients were randomized in this study. Pre-treatment bulk RNAseq of primary tumors was conducted for 754 patients. For 80 patients, bulk RNAseq analysis of a metastastic biopsy was conducted. For these 80 pairs, DNA alterations were assessed in pre-treatment and at recurrence using FoundationOne.

  Dataset EGAD50000001827

• Machine learning guided signal enrichment for ultrasensitive plasma tumor burden monitoring

  Development of a novel machine learning guided ctDNA detection platform for use in liquid biopsy detection and therapeutic monitoring of solid tumors in several clinical contexts. Included are WGS alignments from our study.

  Study EGAS00001007306

• DAC for "Transcriptome analysis of human iPSC-derived microglia in a novel human 3D cortical tissue model"

  scRNA-seq analysis of human iPSC-derived microglia in a novel, human in vitro 3D cortical tissue model. Samples include three distinct conditions (each as biological duplicates): wild-type microglia extracted from cultures after 1 month (WT_1mo) and 3 months (WT_3mo) of culturing, as well as knock-in microglia extracted 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).

  Dac EGAC50000000303

• Mutational Analysis of Colorectal PDX models (2017-05-11)

  Targeted exome sequencing of patient derived xenografts from primary colorectal tumours and liver metastases. This dataset contains all the data available for this study on 2017-05-11.

  Dataset EGAD00001003334

• Fastq and reference alignment of 19 samples for defining structural variation associated with breast cancer susceptibility by long-read genome sequencing

  Long-read genome sequencing performed on the Oxford Nanopore Technologies' PromethION to resolve variants underlying breast cancer susceptibility in sixteen individuals with pathogenic germline SVs in BRCA1, BRCA2, CHEK2 or PALB2.

  Dataset EGAD00001008690

• RNA-Seq dataset for Malignant rhabdoid study

  Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.

  Dataset EGAD00001011819

• CUT&RUN/ChIP-Seq dataset for Malignant rhabdoid study

  Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.

  Dataset EGAD00001011821

• DAC for the study EGAS00001003572

  Dac EGAC00001001174

• Piloting exome resequencing in consanguineous families with homozygosity mapping intervals

  This pilot study aims to generate pilot data to inform future study designs in consanguineous families or inbred populations by resequencing the exome of six individuals from five families with neurodevelopmental diseases. For all of these families a single mapping interval containing the causal variant has previously been identified.

  Study EGAS00001000024

• Cell-free DNA methylome and fragmentome analysis for disease relapse monitoring in patients with Ewing Sarcoma

  We conducted whole-genome and methylome sequencing of cfDNA from 87 serial samples of 23 patients with EwS and 3 patients with CIC-rearranged sarcoma (CIC). With EwingSign, a new machine learning model, we identified EwS or CIC in a test set for 11 out of 16 patients at diagnosis and 15 out of 18 clinically confirmed relapse events. 0 out of 24 non-cancer controls were detected positive with EwingSign.

  Study EGAS50000001415