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• Somatic_mutation_and_clonal_evolution_in_premalignant_lung_disease

  In this study we aim to characterise the landscape of mutation and clonal selection in normal lung and premalignant lung disease. The study combines targeted sequencing and whole-genome sequencing of microbiopsies of lung and bronchial epithelium. The range of patients studied will include healthy individuals, both smokers and non-smokers, and patients with premalignant lung disease.

  Study EGAS00001002340

• RNA-seq of iPSC-derived hepatocyte-like cells

  We performed RNA-seq on polyA-enriched mRNA isolated from the original liver biopsy tissue (Liver tissue), primary liver cells (PLC), hepatocyte-like cells (HLCs) differentiated from induced pluripotent stem cells (iPSCs), and iPSCs. RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation protocol (ref. RS-122-2101, Illumina, San Diego CA, US) and sequenced using the Illumina HiSeq2500 platform following the manufacturer’s protocol. Samples were sequenced in paired-end mode to a length of 2x76 base pairs. Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files.

  Dataset EGAD00001003770

• Epigenomic profiling and transcriptomic profiling of LUAD patients tumor tissues and tumor adjacent tissues

  To provide an in-depth understanding of the epigenomic heterogeneity of LUAD, we here investigated the H3K27ac histone modification profiles of tumors and adjacent normal lung tissues from 42 LUAD patients and explored the role of epigenetic alterations in LUAD progression. We also investigated transcriptomic alterations among 36 patients tumor tissues.

  Study EGAS00001005132

• Multi-omics analyses of airway host-microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions

  The mechanistic role of the airway microbiome in chronic obstructive pulmonary disease (COPD) remains largely unexplored. We present a landscape of airway microbe-host interactions in COPD through an in-depth profiling of the sputum metagenome, metabolome, host transcriptome and proteome from 99 COPD patients and 36 healthy individuals in China.

  Study EGAS00001006398

• TCR β-chain repertoire characterization of regulatory and conventional T cells in peripheral blood from breast cancer patients and healthy individuals.

  Identification of tumor-specific effects on peripheral TCRβ repertoire formation in humans, investigation of the clonal origin of regulatory T cells in breast cancer patients and impact analysis of the tumor-specific conversion of conventional T cells into induced regulatory T cells on the peripheral Treg repertoire in humans.

  Study EGAS00001002699

• TCR β-chain repertoire characterization of regulatory and conventional T cells in breast tumors from breast cancer patients.

  Identification of tumor-specific effects on peripheral TCRβ repertoire formation in humans, investigation of the clonal origin of regulatory T cells in breast cancer patients and impact analysis of the tumor-specific conversion of conventional T cells into induced regulatory T cells on the peripheral Treg repertoire in humans.

  Study EGAS00001004671

• Neurodevelopment_Nantes_hospital

  The neurodevelopmental team in the genetics unit of Nantes hospital focus on the identification on new genes causing neurodevelopmental disorders through whole-genome and transcriptomics sequencing.

  Dac EGAC50000000542

• Expression profiling of Gorlin iPSCs in the osteoblast induction culture

  In this study, we utilized human induced pluripotent stem cell (iPSC)-based models of the two diseases, named Gorlin syndrome and McCune Albright synfrome, to understand the roles of Hh signaling in osteogenesis, especially in mineralization. To examine which signaling pathways and genetic networks were affected by Gorlin syndrome-associated PTCH1 mutation in human osteoblastogenesis, we performed RNA sequencing (RNA-seq) analysis in the osteoblast induction culture of WT and Gorlin iPSCs.

  Study JGAS000218

• The origin of post-transplant clonal hematopoiesis can be traced to prenatal development.

  Clonal hematopoiesis (CH), a prevalent and premalignant state in the elderly, can occur in young individuals under selective pressures such as hematopoietic cell transplantation (HCT). However, the origin of CH and mutational processes underlying CH driver mutations in young individuals remain unclear. Here, we used genome-wide somatic mutation profiles to retrospectively trace the origin of DNMT3A-mutant CH in three individuals, 14-41 years after childhood HCT.

  Study EGAS50000000919

• ERDERA Diagnostic Research Workstream DAC

  The ERDERA Diagnostic Research Workstream DAC decides on data access requests according to the principles defined in the ERDERA Data Sharing Framework Agreement.

  Dac EGAC50000000728

• Antibody Repertoires in CVID

  The data consist of the DNA sequences of antibody gene rearrangements from peripheral blood human B cells of subjects with Common Variable Immune Deficiency (CVID) and healthy controls subjects.

  Study phs000934

• Integrated diagnosis based on transcriptome analysis in suspected pediatric sarcomas

  We performed RNA-sequencing in 47 patients with suspected pediatric sarcomas, to evaluate the potential utility of RNA-seq in the diagnostic process of pediatric sarcoma.

  Study JGAS000284

• Tumor cells metabolically resist immune-checkpoint therapy by macrophage efferocytosis-mediated fatty acid recycling

  Tumor cells metabolically adapt to the nutrient-deprived tumor microenvironment (TME). However, the metabolic plasticity underlying immune-checkpoint blockade (ICB) adaptation remains unclear.

  Study EGAS50000001416

• Angiosarcoma_follow_up_study

  A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

  Study EGAS00001000405

• Kidney_Single_Cell_Study

  We intend to use single cell transcriptome analysis to explore the heterogenity of different cell types within the kidney.

  Study EGAS00001002325

• Chromatin_Profiling_in_Twins

  50 lymphoblastoid cell lines of adult female Twins which are part of the MuTHER study, processed with the FAIRE assay in order to generate maps of open chromatin.

  Study EGAS00001000097

• Angiosarcoma_follow_up_2_validation_study

  A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

  Study EGAS00001000518

• Covid19 WGS BAM files

  The Samples were collected from Saint James's Hospital, Dublin, and after informed consent Extracted Genomic DNA samples were prepared and sequenced using the Automated Illumina TruSeq PCR-free methodology.

  Study EGAS00001007048

• DECONVOLUTION OF HEMATOPOIETIC STEM/PROGENITOR CELL SIGNALING IN HUMAN AML

  A comprehensive taxonomy of the predicted interactions between LEPR + stromal niches, HSPCs and adaptive/innate immune cells in the human NBM and AML

  Study EGAS00001007330

• Latency and interval therapy affect the evolution in metastatic colorectal cancer

  The cohort of 15 patients included ten patients with available tissue from the primary tumor and ≥1 metastatic site, four patients with pairs of metastases only, and one patient with an anastomotic recurrence five years after initial resection of the primary tumor

  Dataset EGAD00001005226

• RNAseq of resident memory T cells from human lung tumor

  This dataset includes the RNA sequencing of 14 samples. Samples are FACS sorted CD8+ T cells expressing or not the integrin CD103. The paired samples (TRM and non-TRM) were sorted from the tumor of 7 lung cancer patients.

  Dataset EGAD00001006812

• Cancer Genetic Markers of Susceptibility (CGEMS) Prostate Cancer Genome-Wide Association Study (GWAS) - Primary Scan (Stage 1) - PLCO Screening Trial

  The Cancer Genetic Markers of Susceptibility (CGEMS) prostate cancer genome-wide association study (GWAS) included genotyping approximately 550,000 SNPs (Phase 1A with HumanHap300 and Phase 1B HumanHap240, both from Illumina, San Diego, CA) in 1,172 prostate cancer patients and 1,157 controls of European ancestry from the Prostate, Lung, Colon and Ovarian (PLCO, http://www.cancer.gov/prevention/plco/) Cancer Screening Trial. The original analysis published in Nature Genetics [PMID: 17401363] included 2,282 subjects. After improvement and revisions of the original analysis, 2,252 subjects were submitted to dbGaP.

  Study phs000207

• ARID1A Mutations in Endometriosis-Associated Ovarian Carcinomas

  We have sequenced the whole transcriptomes of 18 ovarian clear-cell carcinomas and 1 ovarian clear-cell carcinoma cell line and found somatic mutations in ARID1A (the AT-rich interactive domain 1A [SWI-like] gene) in 6 of the samples. ARID1A encodes BAF250a, a key component of the SWI–SNF chromatin remodeling complex. We sequenced ARID1A in an additional 210 ovarian carcinomas and a second ovarian clear-cell carcinoma cell line and measured BAF250a expression by means of immunohistochemical analysis in an additional 455 ovarian carcinomas

  Study EGAS00000000075

• Clonal evolution of metastatic colorectal cancer under anticancer therapies

  To investigate the clonal evolution of metastatic CRC at the single-cell level, we performed WGS in 58 clonal organoids and 18 fresh-frozen (FT) bulk-tissue samples from surgically resected primary and metastatic tumors before and after anticancer therapies in 6 patients. This approach enabled detailed phylogenetic reconstruction of individual clones. We discovered the timing and burden of treatment-related mutations as well as the heterogeneous evolution in driver mutations and genomic rearrangements in late-stage clonal evolution under anticancer therapies in metastatic CRC.

  Study EGAS50000001023

• IgM heavy chain V(D)J library sequencing using varied PCR parameters

  When amplifying the rearranged V(D)J genes encoding antigen receptors during adaptive immune receptor repertoire sequencing (AIRR-seq), each cycle of the PCR can produce spurious “chimeric” hybrids of two or more different template sequences. To test the effects of PCR protocol variation on chimera formation in AIRR-seq, we produced IgM heavy chain V(D)J repertoire libraries under 8 conditions, varying the number of PCR cycles, indexing PCR template, input RNA, and extension time. Three donors were sequenced using all 8 conditions.

  Study EGAS50000001037