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• 3' mRNA- sequencing bams

  This project stores bam files from 3'RNA-seq from oesophageal adenocarcinoma at different timepoints during neoadjuvant treatment (prior, during, post treatment), which were used to analyse evolutionary and phenotype dynamics in oesophageal adenocarcinoma. Samples were collected within the clinical MEMORI trial.

  Study EGAS50000000242

• scRNA-seq data set for 13 AML patients

  This dataset includes single cell (sc)RNA-seq of N=13 AML patients. The dataset includes bam files that have been purged of reads mapping to cells where a majority of the reads from that cell mapped to the human genome. All scRNA-seq data were generated using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) from 10X Genomics.

  Dataset EGAD50000001346

• RNA-Sequencing data of Fusobacterium nucleatum treated CAFs and HT-29 tumor spheroid exposed to Fusobacterium nucleatum treated CAFs conditioned medium.

  RNA-Sequencing data of CAFs (patient derived CAF180 and CAF181 as well as the CT5.3 CAF cell line) and HT-29 tumor spheroid samples performed in the context of the study of the interaction of Fusobacterium nucleatum with CRC CAFs. Fusobacterium nucleatum interacts with cancer-associated fibroblasts to enhance colorectal cancer progression

  Dataset EGAD50000001614

• University of Sydney Thyroid Cancer Data Access Committee

  This Data Access Committee (DAC) manages access to genomic data generated by the Thyroid Cancer Research Group at the University of Sydney and Royal North Shore Hospital. The DAC will evaluate data access requests to ensure they align with participant consent and the conditions approved by the Northern Sydney Local Health District Human Research Ethics Committee. Requests will be reviewed for scientific validity, alignment with the original consent, and compliance with institutional and regulatory data governance policies.

  Dac EGAC50000000661

• Single-cell gene expression profiling of human iPSCs-derived cortical organoids

  To investigate the relationships between cerebral cortical organoid morphological characteristics and cellular composition, we morphologically classifi ed human iPSC-derived cortical organoids and analyzed the cellular makeup of each morphological type by single-cell gene expression profi ling.

  Study JGAS000726

• Aberrant (pro)renin receptor expression induces genomic instability by chromatin remodeler SMARCA5 disruption during the pancreatic ductal adenocarcinoma

  The aim of the present study is to elucidate whether aberrant (P)RR expression induces genomic instability in human pancreatic ductal epithelial (HPDE) cells, which are transforming into pancreatic ductal adenocarcinoma (PDAC).

  Study JGAS000143

• Somatic L1 retrotransposition mapping in high-grade serous ovarian carcinoma using LDI-PCR/Nanopore-sequencing

  Somatic L1 retrotransposition was mapped in high-grade serous carcinoma (HGSC) tumors using LDI-PCR/Nanopore-seq method. This method identifies somatic L1 insertions originating from two active L1 loci at chr22q12.1 and chrXp22.2. Multiple tumors from the same patient were utilised to understand L1-mediated intrapatient heterogeneity. Long-read data generated by LDI-Nanopore sequencing was aligned to the reference genome (GRCh38).

  Dataset EGAD50000001707

• Target bisulfite sequencing of uterine cervical cancer

  We performed targeted bisulfite sequencing of the HLA-A promoter region in cervical tissue samples to investigate DNA methylation patterns that regulate immune recognition and antigen presentation, which may influence viral immune surveillance and malignant transformation in cervical pathology.

  Study JGAS000825

• 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

• Indonesian Genome Diversity Project 3

  Low coverage whole genome sequences were collected to study the population history in Eastern Indonesia, in particular Wallacea and Papua region. We have sequenced the genomes of 254 individuals from 12 Wallacean and 3 Papuan populations spanning this geographical region.

  Study EGAS50000000447

• A study on personalized medicine in genitourinary cancers using genetic biomarkers

  We present a patient with MSI-high castration-resistant PC who showed a remarkable and durable response to pembrolizumab. Whole exome sequencing revealed approximate tumor mutation burden of 61 mutations/Mb as well as biallelic loss of MSH2.

  Study JGAS000510

• Whole genome sequencing, DNA methylation, and gene expression data from gastrointestinal stromal tumor 30 patients

  We performed WGS along with genome-wide DNA methylation and gene expression analyses in 30 GIST cases to determine the genomic and epigenomic differences between KIT exon 11 557���558 deletions and other KIT exon 11 mutations.

  Study JGAS000604

• Whole exome sequence and transcliptomic analysis of tumor tissues with hepatocellular carcinoma and metastatic liver cancer

  We used our pipeline to select neoepitopes with high immunogenicity from the tumor tissues of 46 patients with hepatocellular carcinoma or metastasis of colorectal carcinoma by whole exome sequence and transcriptomic analysis with tumor tissue.

  Study JGAS000507

• 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

• 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

• The analysis of gene mutations in Hematology malignancy

  We analysed the mutations of target genes regarding malignant lymphoma and myeloma to investigate the relationships between clonal evoutions and disease status. The gene mutation analyses using NGS at the point of diagnosis and relapse or proceeding disease.

  Study JGAS000232

• 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

• NeoRhea Bulk RNA and Single nuclei RNA & ATAC

  The aim of this study is to compare baseline and surgery samples of ER+/HER2- early breast cancer patients. Patients have been treated with endocrine therapy in combination with palbociclib. Samples have been collected pre and post treatment.

  Study EGAS50000001403

• Chromatin accessibility of clear cell renal cell carcinoma

  To investigate chromatin accessibility in ccRCC, we performed ATAC-seq in 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions

  Study EGAS50000001325

• 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

• 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

• 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

• 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

• TenK10K Phase 1: Whole Genome Sequencing Alignments

  Whole genome sequencing was performed for 1,925 samples from phase 1 of the TenK10K project. Sequencing was done with Illumina 2 x 150bp chemistry on a NovaSeq 6000 instrument to achieve mean 30x coverage. Sequence reads were aligned to the GRCh38 reference assembly with a fork of DRAGMAP v1.3.1. This dataset is comprised of 1,925 alignment files in cram format, and their corresponding index files.

  Dataset EGAD50000002466