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• DAC for Breast Invasive Lobular Carcinoma CDH1 study

  We developed an artificial intelligence (AI)-model applied to histological images trained using CDH1 biallelic mutations, pathognomonic for breast invasive lobular carcinoma (ILC), as ground truth. We evaluated the performance of the AI-model to predict the presence of CDH1 biallelic mutations and to diagnose ILC. Subsequently, we investigated the molecular underpinning of cases predicted by the model to harbor a CDH1 biallelic mutations but lacking these alterations according to targeted sequencing. We then subjected one ILC lacking CDH1 biallelic mutations and lacking CDH1 promoter methylation to whole genome sequencing (WGS) to determine the molecular basis of its lobular phenotype.

  Dac EGAC50000000333

• Building a Database of Genomic Structural Variants in Japanese population

  Epstein-Barr virus immortalized B-lymphoblast cell lines were obtained through the Japanese Collection of Research Bioresources (Japanese B cell DNA bank), National Institutes of Biomedical Innovation, Health and Nutrition, and cultured at UNITECH Co., Ltd. We extracted genomic DNAs, sequenced them using Nanopore PromethION, and analyzed genomic structural variations.

  Study JGAS000580

• Patient-Derived Follicular Lymphoma Spheroids recapitulate lymph node signaling and immune profile, uncovering galectin-9 as a novel immunotherapeutic target

  RNA-seq data from CD20+ sorted cells obtained from peripheral blood and lymph node Follicular Lymphoma patients. These samples were unstimulated after thawing and additionally, peripheral blood samples were stimulated during 7 days in culture as described in Dobaño-López C et. al.)

  Study EGAS50000000233

• Integrative Analysis of Pediatric Acute Leukemia Identifies Acute Myeloid/T-Lymphoblastic Leukemia Subtype that Spans a T Lineage and Myeloid Continuum with Distinct Prognoses

  Genomic characterization of pediatric patients with acute myeloid leukemia (AML) has revealed age specific mutational spectrums, distinguishing it biologically from adult patients. While gene expression profiling signatures can differentiate subsets of pediatric AML, its clinical utility in risk stratification has remained limited.

  Study EGAS00001004701

• snRNA-seq schizophrenia control Prefrontal cortex

  Human Brodmann Area 8/9 tissue from 43 schizophrenia subjects and 42 control individuals was obtained from three sources, NBB (Netherlands Brain Bank), Craig A. Stockmeier (University of Mississippi Medical Center), Macedonian/New York State Psychiatric Institute Brain Collection (Andrew J. Dwork, Columbia University). All subjects included in the study were matched between the two groups for age, gender, and postmortem interval. Nuclei were isolated and enriched for 85% neuronal nuclei before single nucleus RNA sequencing was performed with 10x Genomics Chromium Single Cell protocol v3.

  Dataset EGAD50000002447

• ovarian cancer sample exome seq

  Tissue samples were collected from 18 ovarian cancer patients. After mechanical and enzymatic dissociation, a part of these tissues underwent growth factoromics analysis. For four cases, single-cell sequencing analysis was conducted under conditions with or without estradiol. Additionally, the remains of the tissues were frozen and subsequently subjected to exome sequencing on 16 of these samples. Sixteen cases were diagnosed as HGSOC, while two samples were clear cell or mucinous type (Extended Data Table 1). All cases were grade 3, and none had received neoadjuvant chemotherapy.

  Dataset EGAD50000002057

• Enzymatic methylation sequencing of rectal mucus from patients suspected to have colorectal cancer

  This dataset contains comprises enzymatic methylation sequencing (EM-Seq) data generated from 208 rectal mucus samples from patients suspected to have colorectal cancer and healthy controls. Targeted CpG sites were enriched using a panel of genes implicated in colorectal cancer, and libraries were prepared with NEBNext EM-Seq prior to Illumina sequencing. Sequencing was performed on the Illumina NovaSeq6000 platform, producing paired-end FASTQ files. These data support analyses of DNA methylation patterns in CRC detection and progression

  Dataset EGAD50000001871

• Sequencing data for the manuscript "Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas"

  Mapping the spatial organization of DNA-level somatic copy number changes in tumors can provide insight to understanding higher-level molecular and cellular processes that drive pathogenesis. We describe an integrated framework of spatial transcriptomics, tumor/normal DNA sequencing, and bulk RNA sequencing to identify shared and distinct characteristics of an initial cohort of eleven gliomas of varied pathology and a replication cohort of six high-grade glioblastomas.

  Dataset EGAD50000001394

• (RNA-seq) Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas

  Raw and processed RNA-seq data from a patient-derived xenograft (yielding 18 samples) and the VOA1066 undifferentiated endometrial carcinoma cell-line (yielding 15 samples). PDX samples were treater with either compound-14, dBRD9, or were untreated. VOA1066 samples were treated with either compound-12, dBRD9, or were untreated. Samples were sequenced on an Illumina NextSeq 500 using 37-bp single-end sequencing. Raw fastq files and gene count tables are included for each sample.

  Dataset EGAD50000001471

• Single-cell multi-omics and mtDNA genotyping of human peripheral blood cells

  This dataset comprises two mtscATAC-seq libraries (customized 10X ATAC-seq) generated from donor M80 and donor H05, and one DOGMA-seq library (customized 10X multiome) generated from donor H05, all derived from primary human peripheral blood mononuclear cells. Patient M80 is an 80-year-old male with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS), while donor H05 is a healthy 5-year-old pediatric donor. The raw FASTQ files have been provided.

  Dataset EGAD50000001489