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• Normal sample for patient SA682

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA682

  Dataset EGAD00001009382

• Normal sample for patient SA683

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA683

  Dataset EGAD00001009383

• Normal sample for patient SA678

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA678

  Dataset EGAD00001009378

• Normal sample for patient SA677

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA677

  Dataset EGAD00001009377

• Normal sample for patient SA673

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA673

  Dataset EGAD00001009373

• Normal sample for patient SA495

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA495

  Dataset EGAD00001009372

• Normal sample for patient SA425

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA425

  Dataset EGAD00001009371

• Normal sample for patient SA423

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA423

  Dataset EGAD00001009370

• Normal sample for patient SA300

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA300

  Dataset EGAD00001009369

• Normal sample for patient SA291

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA291

  Dataset EGAD00001009368

• Normal sample for patient SA289

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA289

  Dataset EGAD00001009367

• Normal sample for patient SA286

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA286

  Dataset EGAD00001009366

• Normal sample for patient SA280

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA280

  Dataset EGAD00001009365

• Normal sample for patient SA239

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA239

  Dataset EGAD00001009364

• Normal sample for patient SA238

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA238

  Dataset EGAD00001009363

• Normal sample for patient SA221

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA221

  Dataset EGAD00001009362

• Tumour sample for patient SA280

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA280

  Dataset EGAD00001009361

• Tumour sample for patient SA291

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA291

  Dataset EGAD00001009360

• Tumour sample for patient SA289

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA289

  Dataset EGAD00001009359

• Tumour sample for patient SA286

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA286

  Dataset EGAD00001009358

• Tumour sample for patient SA495

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA495

  Dataset EGAD00001009357

• Tumour sample for patient SA425

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA425

  Dataset EGAD00001009356

• Tumour sample for patient SA423

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA423

  Dataset EGAD00001009355

• Tumour sample for patient SA300

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA300

  Dataset EGAD00001009354

• Tumour sample for patient SA239

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA239

  Dataset EGAD00001009353

• A96175C

  Whole genome sequencing for single cells for library A96175C 1473 samples; filetype=bam

  Dataset EGAD00001008243

• A96172B

  Whole genome sequencing for single cells for library A96172B 1694 samples; filetype=bam

  Dataset EGAD00001008241

• A96162B

  Whole genome sequencing for single cells for library A96162B 1316 samples; filetype=bam

  Dataset EGAD00001008238

• A96157C

  Whole genome sequencing for single cells for library A96157C 938 samples; filetype=bam

  Dataset EGAD00001008237

• A96149B

  Whole genome sequencing for single cells for library A96149B 1792 samples; filetype=bam

  Dataset EGAD00001008235

• A96149A

  Whole genome sequencing for single cells for library A96149A 751 samples; filetype=bam

  Dataset EGAD00001008234

• A96146A

  Whole genome sequencing for single cells for library A96146A 1195 samples; filetype=bam

  Dataset EGAD00001008233

• A96228B

  Whole genome sequencing for single cells for library A96228B 1125 samples; filetype=bam

  Dataset EGAD00001008218

• RNA sequencing data of in vitro differentiated megakaryocyte cells transduced with E527K and WT SRC

  RNA sequencing data of in vitro differentiated megakaryocyte cells transduced with E527K and WT SRC. CD34+ hematopoietic stem cells (HSC) were isolated from healthy controls before transduction with WT-SRC and E527K-SRC lentiviral vectors in triplicate and differentiation to MK. Three replicates each of two pools were generated for both WT and E527K SRC transduced cells, resulting in 3 WT pool 1 samples, 3 WT pool 2 samples, 3 E527K pool 1 samples and 3 E527K pool 2 samples for a total of 12 samples. RNA was extracted and sequenced with following parameters: Platform: Illumina HiSeq4000, Library Prep Kit: TruSeq stranded mRNA, Sequencing Kit: Illumina HiSeq4000 100 cycles (76-8-8-7), Fragments: single end / fr-firststrand.

  Dataset EGAD00001008356

• RNA data for medulloblastoma samples (ICGC)

  RNA sequencing data for 170 medulloblastoma tumor samples

  Dataset EGAD00001003279

• GUARDIAN: The Insulin Resistance Atherosclerosis Study (IRAS Classic)

  The Insulin Resistance Atherosclerosis Study (IRAS) was an epidemiologic cohort study designed to examine the relationship between insulin resistance and carotid atherosclerosis across a range of glucose tolerance. Individuals of self-reported Mexican-American ethnicity were recruited in San Antonio, TX and San Luis Valley, CO. Recruitment was balanced across age and glucose tolerance status. GUARDIAN includes 173 individuals from the IRAS. Insulin sensitivity was obtained by FSIGT.

  Study phs001014

• Evolving Cell States and Oncogenic Drivers during the Progression of IDH-Mutant Gliomas

  The study aims to understand the changes in cell states during the progression of IDH mutant gliomas. We generated scATAC-seq data from tumor samples of patients with IDH mutant gliomas, ranging from grade 2 to grade 4, including both IDH mutant oligodendroglioma and IDH mutant astrocytoma samples. Additionally, we have generated scRNA-seq data from patient-derived organoids that were treated with a DNMT1 inhibitor.

  Study phs003697

• Study the genetic susceptibility of esophagus squamous cell carcinomas (ESCC) in high-risk area Henan Chinese

  This study utilized a genetically-enriched cohort of patients with familial ESCC from the high-risk Henan region, located near the Tai-Hang Mountain region in Northern China, to identify high penetrance ESCC predisposition genes using a comprehensive unbiased whole-exome sequencing (WES) strategy. Subsequent validate the prevalence of rare damage variants by targeted gene sequencing in a large sample size.

  Study EGAS00001003423

• scKaryoSeq of CRISPR-Cas9 edited primary human T cells

  To explore T cell-intrinsic driving forces of CRISPR-induced aneuploidy at the TRAC gene locus, we performed scKaryo-seq (Bolhaqueiro et al., Nature Genetics 2019). We compared the impact of the small molecule pifithrin-alpha in activated TRAC KO T cells. In a separate experiment, we determined the effect of pifithrin-alpha on non-activated T cells edited at the TRAC locus or treated with non-targeting Cas9 RNPs.

  Dataset EGAD50000000929

• RNA-seq of STIC lesions and adjacent normal samples

  In this study, we characterize premalignant lesions of the fallopian tube (serous tubal intraepithelial carcinomas) to explore the earliest events of tumorigenesis following mutation of the TP53 tumor suppressor gene. We conduct laser capture microdissection to isolate premalignant cells from adjacent normal cells, and subject isolated tissues to RNA-seq. Our findings reveal the earliest transcriptional changes established during premalignancy within the fallopian tube.

  Dataset EGAD50000000289

• colorectal_epigenome

  Three different types of samples were used: 19 normal adjacent, 17 adenoma and 19 colorectal tumor tissue samples. This included 10 pairs of colorectal cancer and normal samples and 1 pair of adenoma-normal samples of the same patient. Tissue specimens were formalin-fixed paraffin-embedded (FFPE). DNA was isolated using the QIAamp FFPE Tissue kit (Qiagen, Hilden, DE) according to the manufacturer’s instructions. The processed DNA was run on the Illumina Human MethylEPIC® v1.0 BeadChip array.

  Dataset EGAD00010002726

• WES in pleural mesothelioma primary cell lines

  We performed exome sequencing on the largest cohort of patient-derived pleural mesothelioma (PM) cell lines (n=58) to explore their molecular heterogeneity. The analysis recapitulated key features of PM tumors and uncovered novel mutations specific to this cohort. These findings provide insight into the genetic landscape of PM, supporting the identification of potential therapeutic targets and advancing the understanding of its molecular diversity.

  Dataset EGAD00001015409

• Peripheral blood RNA-sequencing in 4,732 participants of the INTERVAL cohort

  We performed bulk RNA-sequencing on peripheral blood collected from 4,732 blood donors recruited as part of the INTERVAL study. Using these data, we mapped gene expression and splicing quantitative trait loci (QTLs). Then, we integrated these data with protein, metabolite and lipid QTLs in the same individuals. The study aimed to identify the shared genetic etiology across transcriptional phenotypes, molecular traits and health outcomes in humans.

  Dataset EGAD00001008015

• 10xchromium 3' v3 sequencing from cerebellum, lung, and heart aligned to GRCh38 genome

  Each run contains single cell RNA-seq data from unbiased sampling of single cells from the indicated human tissue. Single cell suspensions were prepared using enzymatic dissociation followed by tituration. The samples were processed using the 10XChromium 3' v3 sequencing pipeline, sequenced on an Illumina NovaSeq 6000, and analyzed using the cellranger software and aligned to the human GRCh38 genome version 93.

  Dataset EGAD00001006110

• 110 "KOREAN" never-smoker female adenocarcinoma RNA-seq

  All sequencing was performed within the DNAlink (Korea) by using the Solexa sequencing technology (Illumina, San Diego, CA). mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads and was fragmented with fragmentation buffer to an average size of 300 bp. The libraries were prepared by using TruSeq RNA Library Prep Kit v2 (Illumina) and were sequenced on the Illumina HiSeq2000 using the manufacturer’s recommended protocols

  Dataset EGAD00001005358

• Genomic Profiling of Sequentially Acquired Metastatic Sites from an "Exceptional Responder" Lung Adenocarcinoma Patient Reveals Extensive Genomic Heterogeneity and Novel Somatic Variants

  We employed next-generation sequencing to identify somatic alterations in multiple metastatic sites from an "exceptional responder" lung adenocarcinoma patient during his seven year course of ERBB2-directed therapies. The degree of heterogeneity was unprecedented, with ~1% similarity between somatic alterations of the lung and lymph nodes. One novel translocation, PLAG1-ACTA2, present in both sites, up-regulated ACTA2 expression. ERBB2, the predominant driver oncogene, was amplified in both sites, more pronounced in the lung, and harbored an L869R mutation in the lymph node. Functional studies demonstrated increased proliferation, migration, metastasis, and resistance to ERBB2-directed therapy due to L869R mutation and increased migration due to ACTA2 overexpression. Within the lung, a nonfunctional CDK12, due to a novel G879V mutation, correlated with down-regulation of DNA damage response genes, causing genomic instability, and sensitivity to chemotherapy. We propose a model whereby a sub-clone metastasized early from the primary site and evolved independently in lymph nodes.

  Study phs001159

• Inhibition of Cbl-b restores effector functions of human intratumoral NK cells

  This study investigates the efficacy of a Cbl-b inhibitor compound in enhancing and reinvigorating the activity of human dysfunctional NK cells.

  Study EGAS50000000574

• BipEx_Ophoff_Amsterdam

  "BipEx_EGAS00001005853_Ophoff_Amsterdam Bipolar Disorder Exomes. This research project was a collaboration between UCLA and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 1,026 Bipolar case/control samples from collaborators in the Netherlands and UCLA. Genomic DNA from each sample was sequenced to a mean depth of 20x."

  Dac EGAC50000000137

• BipEx_Posthuma_Amsterdam

  "BipEx_EGAS00001005857_Posthuma_Amsterdam Bipolar Disorder Exomes. This research project was a collaboration between VU and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 943 Bipolar case/control samples from collaborators in the Netherlands. Genomic DNA from each sample was sequenced to a mean depth of 20x."

  Dac EGAC50000000143

• Stem-like peripheral helper T cells seed their effector counterpart in rheumatoid arthritis

  The dynamics of helper T cells in the synovium of rheumatoid arthritis was investigated using scRNA-seq, scTCR-seq, and spatial transcriptome.

  Study JGAS000774

• Whole genome sequencing analysis of esophageal squamous cell carcinoma

  Whole genome sequencing analysis of esophageal squamous cell carcinoma and the association of their genomic features with the response of neo-aduvant chemotherapy

  Study JGAS000155

• Nanopore sequencing of FSHD, BAMS and healthy control fibroblast cell lines

  The goal was to resolve the complex genetic and epigenetic structures of D4Z4 alleles, a macrosatellite whose desilencing results in FSHD.

  Study EGAS50000001065

• An immune response network associated with blood lipid levels

  Genome-wide genotyping was performed on a population-based cohort from the capital region of Finland using the Illumina 610-Quad SNP microarray

  Study EGAS00000000086

• WES sequencing to characterize ALK

  This exome sequencing study aims to investigate the impact of the K1150dup mutation on lorlatinib progression and to explore potential therapeutic strategies to overcome resistance.

  Study EGAS50000001778

• PFA ependymoma cancer study

  Sequencing data related the PFA ependymoma study (Michealraj et al., Cell 2020), a lethal glial malignancy of the hindbrain found in babies and toddlers.

  Study EGAS00001004312

• DNA-methylation variability in normal mucosa of patients with adenomatous polyps: a marker of field cancerization

  A study linking DNA methylation modifications in the normal mucosa of the right colon in individuals with adenomatous polyp formation

  Study EGAS00001007666

• Whole genome bisulfite sequencing on 10 multiple myeloma cases

  Data quality control and adaptor-trimmed were performed with the Trimomatic tool. Paired-reads were mapped to the hg19 human reference with methylCtools aligner.

  Study EGAS00001004346

• Data containing genome-wide SNP data from Northwestern Amazonia

  Provide new insights about the population history of NWA and identify the impact of intense population contact on patterns of genetic variation

  Study EGAS00001006767

• RNA Dataset

  The RNA dataset includes 5 samples analyzed with the Oncomine Comprehensive Assay (OCA) panel. After library preparation, sequencing was performed on the Ion Torrent S5 System, generating FASTQ files. The analysis captures gene fusions and splice variants relevant to oncogenic processes. (idem)

  Dataset EGAD50000002502

• PREDO_EGA_methylation_data_and_gestation_ages

  This data set contains two data files. First data file (file name: PREDO_GA_EGA_methylation_data.csv) includes methylation data from 485512 sites accross human genome from 96 individuals acquired from Illumina 450K -chip. The other data file (file name: PREDO_GA_EGA_phenotypes.csv) contains the gestation ages and the genders of the 96 samples.

  Dataset EGAD00010001003

• Somatic point mutation data from microsatellite unstable colorectal cancers

  The dataset contains the somatic point mutation data from the exome-targeted region of 36 exome or whole genome sequenced microsatellite unstable colorectal cancers and the somatic point mutation data from 93 additional MiSeq sequenced microsatellite unstable colorectal cancers.

  Dataset EGAD00001004281

• bulk Exome-seq of the 5 HCC patients which also have the single cell T cell RNA-seq data

  bulk Exome-seq data of the 5 HCC patinets. Single cell RNA seq data of these patients was under the accession number EGAD00001003337

  Dataset EGAD00001004149

• Fragmentomics profiling and quantification of plasma Epstein-Barr virus DNA enhance prediction of future nasopharyngeal carcinoma.

  This study evaluated the clinical utility of fragmentomics analysis of plasma Epstein-Barr virus (EBV) DNA in nasopharyngeal carcinoma (NPC) screening. The first-round EBV-positive blood samples from a two-round large-scale prospective NPC screening cohort were analyzed. The EBV DNA of subjects who developed NPC in the second round displayed a distinctive mononucleosomal size pattern, an NPC-associated end motif profile, and aberrations in methylation deduced by fragmentomics-based methylation analysis (FRAGMA). Subjects with these aberrant fragmentomics features and higher EBV DNA quantity showed a dramatically increased risk of NPC development, demonstrating the potential of plasma DNA fragmentomics in predicting future cancer risk.

  Study EGAS50000000395

• Identification of genetic mutations characteristic for recurrence of serous ovarian cancer.

  Establishment of novel therapeutic strategy to overcome intractable cancer by molecular profiling of serous ovarian cancer

  Study JGAS000104

• Massachusetts General Hospital Cancer Center DAC for single cell RNA-seq data from small cell lung cancer primary tumors and CTCs

  single cell RNA-seq data from 10 small cell lung cancer primary tumors and circulating tumor cells of three small cell lung cancer patients

  Dac EGAC50000000808

• TRACERx NSCLC - whole genome sequencing for ctDNA study

  An ultra-sensitive and specific ctDNA assay provides novel pre-operative disease stratification in early stage lung adenocarcinoma

  Study EGAS50000000313

• Buccal Sample Methylation for Breast Cancer Detection

  This study encompasses buccal sample DNA methylation (IlluminaMethylationEPIC array) from breast cancer cases and healthy age-matched controls.

  Study EGAS00001007658

• cell-free Methylated DNA by Immunoprecipitation and Sequencing (cfMeDIP) of human meningioma samples.

  Raw data for cell-free Methylated DNA by Immunoprecipitation and Sequencing (cfMeDIP) of human meningioma samples.

  Dataset EGAD50000002214

• Long-read RNA-sequencing of three adult human neural retina samples for 17 lncRNA loci.

  Long-read direct cDNA sequencing (Oxford Nanopore Technologies) of three independent post-mortem human retina samples of 17 lncRNA loci.

  Dataset EGAD50000001402

• SCLC MeDIP-seq

  Methylation profile of 33 patients with small cell lung cancer (SCLC) for both, tumour and normal lung samples using MeDIP-seq.

  Dataset EGAD50000000724

• OncoScan SNP data set for localized follicular lymphoma (lFL)

  149 unpaired initial tumor samples (133/149 FFPE and 16/149 fresh frozen samples) of lFL patients measured with OncoScan SNP microarrays, Affymetrix CEL intensity data file types (Thermo Fisher Scientific, Waltham, Massachusetts, USA)

  Dataset EGAD00010002593

• P50_P681_P763_PTC209_DMSO_24h_48h_72h_Illumina HT12v4_Gene_Expression.xlsx

  Expression dataset for DAC+PTC209 treated CD34 sorted primary CML bone marrow samples

  Dataset EGAD00010002210

• Oncoscan SNP arrays for study "Molecular and functional profiling of plasmablastic lymphoma"

  1 cell line and 82 Oncoscan SNP tumor initial samples, zipped Affymetrix CEL file types, Oncoscan CNV FFPE Assay Kit, Thermo Fisher Scientific GeneChipTM Scanner 3000 7G

  Dataset EGAD00010001978

• Clinical data

  Clinical data from AVANT: Clinical data include race, age, sex, baseline ecog, tumor stage, node status, treatment arm, KRAS and BRAF mutation status, tumor location, concensus molecular subtype, overall survival and disease free survival for 797 patients across AVANT.

  Dataset EGAD00001009727

• Dataset for Stromal-induced epithelial-mesenchymal transition induces drug resistance in acute lymphoblastic leukemia

  RNA-seq was performed to compare gene expression profiles between 11 patient adherent ALL samples and nonadherent ALL samples.

  Dataset EGAD00001009056

• Genomic determination for Homologous Recombination Deficiency (HRD) by shallow Whole Genome Sequencing (sWGS)

  Homologous recombination deficiency (HRD) score in a large cohort of 55 triple-negative breast cancer PDX

  Dataset EGAD00001008839

• B15PON dataset

  Organoid cultures derived from normal colon and/or colorectal adenomas and/or colorectal carcinomas. RNA and DNA was isolated from these cultures for genome wide profiling.

  Dataset EGAD00001008411

• GCAT| PCAs GCATcoreSpain V2

  First 20 principal components of 4988 genotyped GCAT Cohort individuals with Infinium Multi-Ethnic Global (MEGAEX2) array, with data for Cr1-22. Plink files with QC and imputed (SHAPEIT+IMPUTE).

  Dataset EGAD00001007730

• Clinical dataset (new)

  ctDNA guiding adjuvant immunotherapy in urothelial carcinoma (Nature 2021). ABACUS clinical data cut (2020) used in 2021 paper: Clinical data include PCR, RFS_months, RFS_event, and OUTCOME for 40 patients in ABACUS with ctDNA data.

  Dataset EGAD00001007578

• Single-cell RNA-seq data from metastatic ovarian cancer for quality control study

  This study includes treatment-naïve fresh tissue sample from 4 HGSOC patients.

  Dataset EGAD00001006984

• RNAseq for brainstem glioma

  RNAseq on Illumina HiSeq X Ten of brainstem glioma primary tumor sample

  Dataset EGAD00001006094

• Whole Exome Data for two affected individuals in a family with severe congenital neutropenia (SCN).

  Raw Whole Exome Sequencing data from Blood samples drawn from related Female participants presenting severe congenital neutropenia.

  Dataset EGAD00001005937

• RNA Sequencing of human fetal brain (FBSeq)

  FastQ files with paired-end RNAseq data for human fetal brain homogenate from 120 samples (12-19 post-conception weeks).

  Dataset EGAD00001004363

• Set of Structural Variants and Indels for GoNL samples

  These files contain indels and structural variants on 769 GoNL samples (SV release 6, 2016-05-25).

  Dataset EGAD00001002261

• Analysis of somatic mutations in normal blood, AML and MDS samples

  Targeted pulldown of genes known to be recurrently mutated in AML & MDS from patient and normal samples using Agilent Sureselect and for some cases also using Illumina Truseq technology.

  Dataset EGAD00001002180

• Identifying new diagnostic and treatment pathways for patients with unclassifiable sarcomas

  Whole genome sequencing of tumour normal pairs of human undifferentiated sarcomas.

  Dataset EGAD00001003216

• WGS data for medulloblastoma samples (SJMB)

  WGS data of medulloblastoma tumor/control pairs.

  Dataset EGAD00001003126

• eFORGE software tool BLUEPRINT dataset

  DNase accessibility data for BLUEPRINT consortium immune cells included in eFORGE software tool

  Dataset EGAD00001002713

• 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

• GWAS membranous nephropathy Stanescu et al., 2011 UK cohort, chr2 region of interest, imputed

  334 biopsy-confirmed membranous nephropathy (MN) cases and 349 ethnically matched healthy controls: the British cohort of the Stanescu et al., 2011 GWAS. Genotyped and imputed region of interest on chromosome 2 (hg19 chr2:160500000-161500000), as used to determine Neanderthal introgression near the PLA2R1 MN risk locus (lead SNP: rs4664308).

  Study EGAS00001007700

• Nasopharyngeal RNASeq Comparing SARS-CoV-2+ Patients and SARS-CoV-2 Negative Control Subjects

  The goal of this analysis was to compare RNAs enriched in the upper respiratory tract of SARS-CoV-2 patients and SARS-CoV-2 negative controls. RNA-sequencing of RNA isolated from the viral transport medium associated with nasopharyngeal swab samples from SARS-CoV-2+ patients and SARS-COV-2 negative controls.

  Study phs002433

• RNA sequencing of genetically modified human iPSCs modeling patients with autism spectrum disorders (ASD)

  We generated two genetically modified iPSC lines. In each line, a single promoter variant identified in a patient with autism spectrum disorder (ASD) was introduced by using the CRISPR/Cas9 system. These mutant lines were analyzed by RNA-seq together with control lines to assess the impact of the introduced variant.

  Study JGAS000651

• 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

• Spinocerebellar ataxia type 3 RNA-sequencing study

  RNA-Sequencing from human post-mortem Spinocerebellar ataxia type 3 patients. This sequencing experiment was carried out to validate that the transcriptional changes of an Ataxin-3 knock-in mouse model (expressing an expansion of 304 CAG/CAAs either heterozygous or homozygous in the murine Ataxin-3 locus) represent that transcriptional changes seen in the human disease.

  Study EGAS00001004241

• 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

• ADAPTeR Study: scRNA and scTCR data from TILs from two ccRCC patients treated with anti-PD1

  TILs were extracted from two ccRCC patients treated with (Nivolumab) anti-PD1, one was responsive to treatment, the other non-responsive. IgG4 staining was used to separate cells into anti-PD1 bound and unbound, the samples then underwent paired scRNA and scTCR sequencing on the 10x Genomics platform.

  Study EGAS00001005640

• Whole-exome sequencing of paired tumour/blood of 58 T1 stage bladder cancer patients

  To understand the molecular determinants that underpin the clinical heterogeneity of non-muscle-invasive bladder cancer (NMIBC) we carried out whole-exome sequencing (WES) of stage T1 bladder tumours to identify prognostic biomarkers and novel therapeutic targets. The study includes paired tumour/blood samples of 58 T1 stage bladder cancer patients.

  Study EGAS00001005765

• 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

• Epi2Diag

  Genomic DNA was extracted from whole blood and bisulfite converted using the EZ DNA Methylation Lightning Kit (Zymo research). DNA methylation profile was then derived using Illumina’s Infinium EPIC array v2.0. in accordance with the manufacturer’s protocol at the ASGARD-Rouen genomic platform (Inserm U1245, University of Rouen and Rouen University Hospital, Rouen France) on an Illumina NextSeq550 scanner.

  Study EGAS00001008070

• 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