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• Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq

  Gluten-specific CD4+ T cells drive the pathogenesis of celiac disease and circulating gluten-specific T cells can be identified by staining with HLA-DQ:gluten tetramers. In this first single-cell RNA-seq study of tetramer-sorted T cells from untreated celiac disease patients blood, we found that gluten-specific T cells showed distinct transcriptomic profiles consistent with activated effector memory T cells that shared features with Th1 and follicular helper T cells. Compared to non-specific cells, gluten-specific T cells showed differential expression of several genes involved in T-cell receptor signaling, translational processes, apoptosis, fatty acid transport, and redox potentials. Many of the gluten-specific T cells studied shared T-cell receptor with each other, indicating that circulating gluten-specific T cells belong to a limited number of clones. Moreover, the transcriptional profiles of cells that shared the same clonal origin were transcriptionally more similar compared with between clonally unrelated gluten-specific cells.

  Study EGAS00001005517

• Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells

  Studies over the past decade characterized murine regulatory T cells (Tregs) with the capacity to promote tissue regeneration. In humans, such a population of tissue-repair Treg cells has not been discovered yet. Using single-cell chromatin accessibility profiles of murine and human tissue Treg cells, we defined a species-conserved and microbiota-independent repair Treg signature, with a prevailing footprint of the transcription factor BATF. Combining this signature with gene expression profiling and TCR fate mapping, we identified a population of tissue-like Treg cells in peripheral blood, characterized by the expression of BATF, CCR8 and HLA-DR. Human BATF+CCR8+ Treg cells from normal skin and adipose tissue shared features with tumor-resident Treg and tissue T-follicular helper (Tfh) cells. Inducing a Tfh-like differentiation program in naive Treg cells partially recapitulated human tissue Treg characteristics, including enhanced wound healing potential

  Study EGAS00001004900

• Genome Landscape of High-Grade Serous Ovarian Cancer

  Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.

  Study EGAS00001000397

• Spatially resolved niche and tumor microenvironmental alterations in gastric cancer peritoneal metastases

  Peritoneal metastases (PM) in gastric cancer (GC) portend a poor prognosis, yet our understanding of tumor microenvironmental (TME) characteristics associated with GCPM remain limited. Here, we analyzed intrinsic genomic alterations and transcriptomic programs predictive of GCPM in a prospective cohort of 248 patients, identifying CDH1, PIGR, and ELF3 mutations as predictors. By inspecting the spatial dynamics of the TME, we find that tumor compartment infiltration of pro-tumorigenic cell types such as inflammatory cancer-associated fibroblasts (CAFs) predict peritoneal recurrence. Next, in a cross-sectional study of 205 samples from 55 patients, distinct pathways and immune compositions in GCPM relative to liver metastases highlight the TME's significance in transcoelomic metastases. Notably, several putative therapeutic targets exhibited distinct expression patterns between PTs and PMs. Our findings highlight transcriptomic variations and niche reprogramming in the GCPM peritoneal environment, revealing roles of myeloid dendritic cells, effector memory CD8+ T cells, and CAFs in metastatic progression.

  Study EGAS50000000501

• Haemoglobin_E_beta_thalassaemia_in_a_patient_group_from_Sri_Lanka

  Exome sequencing of 32 patient samples from Sri Lanka with the condition haemoglobin E beta thalassaemia

  Study EGAS00001000626

• RNA-sequencing from duodenal bipsies of Celiac disease patients

  Total RNA was extracted from the PaxFPE biopsy specimens (n = 116)

  Study EGAS50000000337

• Genomic profiling of two pathogenic germline truncating variants of BRCA2 confer different haploinsufficiency phenotype

  Observation of the loss of heterozygosity of BRCA2

  Study EGAS50000000613

• MIBS MGS

  Metagenomic sequencing of the human gut in Maastricht IBS studies, cases and controls.

  Study EGAS00001001924

• RNA-seq of human embryonic heart, lung, and cerebellum

  Characterization of cell types in the human embronic heart, lung, and cerebellum.

  Study EGAS00001004375

• miRNASeq profiles from Indian HFrEF Cohort

  The dataset contains miRNA profiling from a cohort of 49 HFrEF patients. The myocardium samples were collected from these patients during heart transplant of LVAD implantation procedure. The RNA samples were collected in RNAlater. Small RNA libraries were prepared using QIAseq miRNA Library Kit, Qiagen and sequenced on Illumina HiSeq4000.

  Dataset EGAD50000001194

• CATNON: IDH-mutant astroctyoma RNA FASTQ

  Raw fastq files obtained by RNA sequencing 138 IDH-mutant astrocytomas included in the CATNON trial. RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue blocks using the RNeasy FFPE kit. RNA sequencing was performed on an Illumina NovaSeq 6000 (GenomeScan BV, Leiden, The Netherlands) with 150bp paired-end reads including UMI tags.

  Dataset EGAD50000000558

• Disease recurrence after pathologic response

  In this study we aim to gain insight into the mechanisms of immune evasion after initial pathologic response to neoadjuvant immune checkpoint inhibition in macroscopic stage III melanoma by pooling data of the neoadjuvant OpACIN, OpACIN-neo and PRADO trials. Therefore we analyzed in-depth paired baseline(n=10) and recurrent tumor samples of the lymph nodes(n=10) and brain metastasis (n=2) through Whole Exome Sequencing (WES) analyses.

  Dataset EGAD50000000700

• Paired-end Whole Exome-seq analysis of the Hypermutation and Malignant Progression in Low-grade Glioma Patients

  113 DNA samples were derived from the tumors of the low grade glioma patients and sequenced using Illumina WES (exome seq) paired-end technology. Dataset contains 113 BAM files aligned to hg19 using BWA v.0.5.9. After mapping duplicated reads were removed, reads were re-aligned around InDels and read base quality score was re-calibrated.

  Dataset EGAD00001005386

• Complete Metagenomics from feces

  Complete Microbiome Metagenomics from feces of 461 IBD patients; The sequencer used was the Illumina HiSeq 2000 with a paired end reads design, reflected in the 2 FastQ format files per sample.

  Dataset EGAD00001004194

• Discovery of resistance mechanisms to the BRAF inhibitor vemurafenib in metastatic BRAF mutant melanoma

  Discovery of resistance mechanisms to the BRAF inhibitor vemurafenib in metastatic BRAF mutant melanoma by massively-parallel sequencing of tumour samples. Comparison of genomic characteristics of pretreatment 'sensitive' to recurrence 'resistant' tumours to identify the genetics of drug resistance.

  Dataset EGAD00001000707

• RNA sequencing data of pediatric hyperdiploid acute lymphoblastic leukemia (set 5)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of five hyperdiploid ALL patients (ALLT-502, ALLK-130, ALLK-134, ALLK-137, ALLK-139). Novogene's internal method was used in directional library preparation including rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002592

• RNA sequencing data of pediatric hypodiploid acute lymphoblastic leukemia

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one hypodiploid ALL patient (ALLT-351). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Ribo-Zero Magnetic Kit (Illumina) was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002605

• First in vivo investigation of the impact of PARP inhibition with rucaparib alone and in combination with atezolizumab: results of the phase Ib COUPLET clinical study in advanced gynecologic and triple-negative breast cancers

  Study EGAS00001006100

• Molecular landscape of C1498 cells

  We characterized the genomic background of C1498 cells by whole genome sequencing analysis.

  Study EGAS50000001284

• Whole Genome Sequencing of Insulinomas

  Whole Genome Sequencing of Insulinomas and paired blood controls from the same patients.

  Study EGAS50000000321

• SCLC tumor sequencing

  In this study we have sequenced the tumor of 28 Small Cell Lung Cancer patients.

  Study EGAS00001003985

• Tumor Profiler AML Study

  Multi-omics data generated from 22 samples from the Tumor Profiler AML cohort

  Study EGAS50000000577

• Targeted_sequencing_of_in_vitro_colonies___bulks

  In this study we will perform targeted sequencing on the bulk samples of in vitro colonies

  Study EGAS00001003175

• Targeted_EMSeq___Development

  Development of a targeted methylation assay to determine the cell-type composition of a sample.

  Study EGAS00001007202

• Single Nuclei RNA sequencing batch 1

  This dataset includes the first 9 PTC samples and 6 ATC samples profiled on the same sequencing flowcell.

  Dataset EGAD00001011366