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• exploration of biomarkers in colorectal cancer

  Targeted therapies based on the molecular and histological features of cancer types are becoming standard practice. To understand the molecular basis of colorectal cancer, we performed CAGE (Cap Analysis of Gene Expression) to quantify promoter activities on 45 colorectal cancers.

  Study JGAS000489

• DNA methylation array analysis of pediatric T-cell acute lymphoblastic leukemia

  Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is rare and its pathogenesis is poorly understood. To investigate epigenetic profiles of pediatric T-ALL, we performed DNA methylation array analysis in 79 cases of pediatric T-ALL.

  Study JGAS000138

• Transcriptome analysis of Fabry disease iPSC-derived cardiomyocytes treated with splice-regulating compound; RECTAS

  In order to investigate transcriptome profiles in response to splice-regulating compounds, iPSC-derived cardyomyocytes were treated with RECTAS and transcriptome study was conducted by RNA-seq. Splicing profiles of cells in each condition were then analyzed.

  Study JGAS000225

• Genome-wide integrative analysis of pediatric pancreatoblastoma

  Pancreatoblastoma is the most common pancreatic malignancy of young children, but its molecular pathogenesis remains poorly understood. To understand the molecular pathogenesis of pancreatoblastoma, we comprehensively analysed the whole exome sequencing, RNA sequencing, SNP array, and methylation array data of pancreatoblastoma.

  Study JGAS000088

• RNA-Seq for SF3B1 splicing signature

  This dataset includes exome-captured RNA-Seq made with exome v8 (Agilent) - library preparation on a MAGNIS XT-HS2 starting from 100ng of RNA. RNA has been extracted from lymphocytes cultures from 2 probands with SF3B1 mutations and 14 controls. All 16 RNA-Seq were sequenced on a single HighOutput flowcell 2x75bp (NextSeq550). Raw fastq files have between 20 and 30M paired-reads.

  Dataset EGAD50000002121

• Bulk RNASeq of metastatic colorectal cancer organoids with ATOH1 knockout

  Bulk RNA sequencing was performed on mCRC organoids subjected to cetuximab treatment, comparing ATOH1 knockout and control conditions. The dataset is intended to elucidate the contribution of ATOH1-regulated secretory cell population to cetuximab persistence mechanisms.

  Study EGAS50000001421

• Bulk RNASeq of metastatic colorectal cancer organoids treated with crenigacestat alone or in combination with cetuximab

  Bulk RNA sequencing was performed on mCRC organoids cultured under untreated conditions or treated with crenigacestat alone or in combination with cetuximab. This dataset was generated to investigate the transcriptional changes associated with combination therapy and to compare these profiles with the adaptive responses observed following cetuximab monotherapy in the corresponding ATOH1 wild-type and knockout organoid models.

  Dataset EGAD50000002061

• Whole-genome sequencing study of uveal melanoma

  Uveal melanoma is the most common primary intraocular cancer, characterized by metastasis-related mortality. Here, we explored whole-genome sequences from 40 primary uveal melanomas to illustrate the landscape of genomic mutations and investigate their association with prognosis.

  Study EGAS50000001603

• 10X single-cell Multiome (RNA+ATAC) of bone marrow-derived HSPC

  10X genomics chromium single-cell ATAC+RNA (Multiome) was use to prepare single-nucleus RNA- and ATAC-seq libraries, sequenced on an Illumina NovaSeq 6000 platform. BAM files are provided. Samples from 6 donors were sequenced after sorting for primitive HSPCs in 5 libraries; each library comprises a single donor, except one with cells from 1 male and 1 female donor.

  Dataset EGAD50000002326

• 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

• WNT7B-reporter organoids sorted

  Transcriptomic data from pancreatic ductal adenocarcinoma (PDAC) organoids to investigate the role of WNT7B. This dataset includes: - Bulk mRNA sequencing of WNT7B-reporter pancreatic ductal adenocarcinoma (PDAC) organoids sorted for cells displaying low, medium and high expression of the reporter

  Study EGAS50000001543

• Transcriptome analysis of human muscle/myofibers carrying the human nemaline myopathy type 6-associated KBTBD13-R408C variant.

  This dataset contains mRNA-seq results from eleven samples from human donors, each sample being composed of 5-10 rebulked fiber type-specific myofibers. This sample set includes; 1) Three FT-I and three FT-IIa rebulked samples from control individuals 2) Three FT-I and two FT-IIa rebulked samples from NEM6 patients with a KBTBD13R408C variant (NP_001094832.1: p.Arg408Cys)

  Dataset EGAD50000002408

• Whole exome sequencing of virus-associated HCC

  To understand comprehensive combinations of molecular alterations and seek for potential therapeutic targets/pathways in virus-associated HCC, we have conducted a whole exome sequencing (in-solution capturing all human coding exons) of 150 pairs of HCC cases.

  Study EGAS00001000389

• HER2_positive_Breast_Cancer_

  We propose to definitively characterise the somatic genetics of HER2+ve breast cancer through generation of comprehensive catalogues of somatic mutations in a number of cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000042

• Genetic_factors_underlying_premature_MI_in_Greek_families_without_vessel_disease

  The study will analyse by exome sequencing 8 Greek family members with an excess of potentially damaging mutations relating to premature MI and no vessel disease, to identify genetic factors underlying this condition. This is a follow on from project GPMI-NVD

  Study EGAS00001000478

• Alternative splicing in Shh-MB

  We analyzed alternative splicing with Shh medulloblastoma. This dataset contains bam files of whole genome sequencing from 4 cases. Genomic DNA was isolated from both tumor and matched control specimens. We performed whole genome sequence on Illumina Hiseq.

  Study EGAS00001003220

• WTCCC2 People of the British Isles (POBI) genotypes

  As part of the WTCCC2 project, approximately 2,900 individuals from the People of the British Isles (POBI) project were genotyped on the Illumina 1.2M array (2,912 samples) and the Affymetrix 6.0 array (2,930 samples).

  Study EGAS00001000672

• Balanced_Brain_Tumour_Whole_Genome_Sequencing

  We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Study EGAS00001000360

• IBDCA_Edinburgh

  In this experiment we have sequenced tumour normal pairs from patients presenting with CRC who have a prior history of inflammatory bowel disease. The idea is to identify driver mutations, new genes and novel pathways associated with the development of these malignancies.

  Study EGAS00001001129

• Predictor_RIO_TNBC

  In this study, samples fom a window study of the PARP inhibitor rucaparib in patients with primary triple negative or BRCA1/2 related breast cancer (RIO trial) will be investigated. Samples will undergo whole genome sequence and analysis, including use of HR Predict.

  Study EGAS00001002805

• Triple_Negative_Breast_Cancer_sequencing

  We propose to definitively characterise the somatic genetics of triple-ve breast cancer through generation of comprehensive catalogues of somatic mutations in a number of cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000161

• Transposome_Bisulfite_Sequencing

  DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform.

  Study EGAS00001000751

• Tumor suppressor miR-133a modulates the prostate cancer epigenome by repressing BAZ2A

  Our study revealed a new subgroup of prostate tumors defined by the expression of a novel prognostic marker, BAZ2A, and the first time to show the establishment of CIMP via an microRNA-epigenetic interaction in prostate tumors.

  Study EGAS00001000568

• Exome sequencing of United Kingdom Brain Expression Consortium samples

  The United Kingdom Brain Expression Consortium studies regulation of gene expression through common and rare variation. One of the main set of samples is compound by bulk brain tissue from 10 brain regions obtained from 134 controls.

  Study EGAS00001002113

• Myeloma WGS

  Most patients with multiple myeloma (MM) die from progressive disease after relapse. To advance our understanding of MM evolution mechanisms, we performed whole-genome sequencing of 80 tumour-normal newly diagnosed pairs and 24 matched relapse tumours from the Myeloma XI trial.

  Study EGAS00001004000