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• Intercellular nanotube-mediated mitochondrial transfer enhances T-cell metabolic fitness and antitumor efficacy

  We found that bone marrow-derived mesenchymal stromal cells (MSC) establish nanotubular connections with T cells in a Talin 2 (TLN2)-dependent manner and leveraged these intercellular highways to supply new mitochondria to CD8+ T cells. In this experiment we analyzed the transcriptional profile of T cells co-cultured with MSC containing MSC derived Mitochondria (MitoPositive), T cells co-cultured with MSC not containing MSC derived Mitochondria and control T cells.

  Study EGAS00001007356

• NEC

  This multi-centre, non-randomized, open-label, phase II trial (NCT03016338), assessed niraparib monotherapy (cohort 1, C1), or niraparib and dostarlimab (cohort 2, C2) in patients with recurrent serous or endometrioid endometrial carcinoma. The primary endpoint was clinical benefit rate (CBR). Secondary outcomes were safety and objective response rate (ORR). Translational research was an exploratory outcome. Potential biomarkers were evaluated in archival tissue by immunohistochemistry and next generation sequencing panel. Feasibility of liquid biopsy by ctDNA was assessed.

  Study EGAS00001007013

• Genome-wide analysis of H3K27me3 occupancy and DNA methlytion in pediatric high-grade glioma

  Genome-wide analysis of H3K27me3 occupancy and DNA methylation in K27M-mutant and H3.3-WT primary pediatric high-grade gliomas (pHGGs) as well as pediatric pHGG cell lines. The study aims to elucidate the connection between K27M-induced H3K27me3 reduction and changes in DNA methylation as well as gene expression.

  Dataset EGAD00001000677

• Targeted exome DNA sequencing of matched brain tumor-normal pairs (ICGC)

  Illumina HiSeq sequence data (with >80x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.

  Dataset EGAD00001000699

• Myeloproliferative Neoplasms (MPN) Targeted Gene Screen

  Pulldown experiments will be performed on a number of patients with Myeloproliferative Neoplasms (MPN). The pulldown will be a bespoke design targeting known mutations, this pulldown will be sequenced and analysed to inform prevalence of mutations and to inform to the possibility of use as a diagnostic tool.

  Dataset EGAD00001000652

• Matched Pair Cell Line Tumour RNAseq

  In this study we will sequence the transcriptome of Verified Matched Pair Cancer Cell line tumour samples. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

  Dataset EGAD00001000630

• Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children

  We investigated 10 female and 14 male SARS-CoV-2 positive children (age range: 0.8 to 18 years). Based on the WHO guidelines, 15 patients were classified as having mild COVID-19, while 7 children were classified as moderate COVID-19 cases. Two children were asymptomatic. 8 female and 10 male SARS-CoV-2 negative children were included as controls (age range: 4 to 16). 12 SARS-CoV-2 positive female and 9 male adults were included ( age range: 27 - 76) together with 13 female and 10 male SARS-CoV-2 negative adult controls (age: 24 - 77). 10 adult COVID-19 patients had mild disease, while 12 had moderate COVID-19. We performed single-cell RNA sequencing experiments.

  Dataset EGAD00001007969

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - structural variation vcf files (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - structural variation vcf files (Mutographs)

  Dataset EGAD00001015389

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - copy number variants (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - copy number variants (Mutographs)

  Dataset EGAD00001015390

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - sequence data (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - sequence data (Mutographs)

  Dataset EGAD00001015386

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - patient metadata files (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - patient metadata files (Mutographs)

  Dataset EGAD00001015387

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - filtered vcf files (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - filtered vcf files (Mutographs)

  Dataset EGAD00001015388

• Contribution of specific cell types to the development of Barrett’s esophagus and carcinoma via germline genetic risk

  We sought to elucidate how individual cell types in Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC) contribute to disease development via germline genetic risk.

  Dac EGAC50000000235

• Genetic architecture of microRNA expression and its link to complex diseases in the Japanese population

  We mapped microRNA expression quantitative trait loci by quantifying microRNA expression using small RNA sequencing.

  Study JGAS000504

• Star-based RNA count files

  To ellucidate gene activity in mRCC, RNA Sequencing data was generated as part of the EuroTarget study. Star aligner 2.7 was used to generate count files

  Dataset EGAD50000002296

• Whole genome sequencing data of relapsed paediatric KMT2A-rearranged acute lymphoblastic leukemia

  Bam-file of the one replased KMT2A-r case. Diagnostic (ALLT-375D) and remission (ALLT-375R) samples can be found from EGA submission EGAD50000001568.

  Dataset EGAD50000001593

• Whole-exome sequencing of acute myeloid leukemias with aberrations of chromosome 7

  This dataset contains the bam files of 60 paired samples of AML and remission samples.

  Dataset EGAD50000000621

• L1-Architect Project Dataset

  Tumours with high and ultrahigh rates of somatic retrotransposition studied in the publication by Zumalave et al. titled Synchronous L1 retrotransposition events promote chromosomal crossover early in human tumorigenesis

  Dataset EGAD50000000607

• Structural variants

  Structural variants assessed in 6 patient samples with varying phenotypes, through the use of sniffles2 with a support parameter of 1 and at a length of 30 bp

  Dataset EGAD50000000741

• scRNA data of multiple myeloma

  Dataset containing 36 samples of multiple myeloma. The sequencing was always paired and performed on Illumina NextSeq 550 and Illumina NovaSeq 6000.

  Dataset EGAD50000000438

• Longitudinal 3'RNA-Seq data from MEMORI trial

  80 bam files generated from 3'RNAseq of tumour biopsies from oesophageal adenocarcinoma. Samples were collected within the clinical MEMORI trial.

  Dataset EGAD50000000357

• N2M2 methylation array data

  Methylation profiling of 228 samples, using the approach described in "Molecularly matched targeted therapies plus radiotherapy in patients with newly diagnosed glioblastoma without MGMT promoter hypermethylation (N2M2/NOA-20 phase I/IIa umbrella trial)"

  Dataset EGAD00010002747

• Average_hypermethylation_TF_sites

  Average hypermethylation on transcription factor binding sites based on nanopolish calls; only positions showing higher methylation than sample’s average methylation at enhancers were included when defining the average methylation level. Data from 6 individuals at different time points.

  Dataset EGAD00010002411

• Methylation array data of thymic epithelial tumors (TC, NET, THYM)

  Methylation microarray data (Illumina 850K) of 52 thymic epithelial tumors. 13 patients with thymoma A and B, 32 thymic carcinoma (TC) and 7 neuroendocrine tumors of the thymus (NET).

  Dataset EGAD00010002355

• Identifying the role of ID3 in DNA repair and maintenance of genome integrity (ATAC-seq)

  Dataset EGAD00001008199