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• HCI-PDX Trial Center for Breast Cancer Therapy

  The HCI-PDX Trial Center for Breast Cancer Therapy study is a collection of patient-tumor samples that are serially established as patient-derived tumor xenografts (human tumor in mouse) and matching organoids. For this study, we describe valuable methods and resources to generate organoids and use them as cost-effective models for precision drug screens. This study leveraged whole-exome sequencing, RNAseq, and SNP-array data to illustrate how the heterogeneity of tumors is preserved in xenograft and organoid models. Sequencing files are provided for whole-exome and RNAseq data. Processed copy number variant calls from the SNP arrays are also available. A full description of the study can be found in the article entitled, "A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology," written by Guillen et al., 2022 in Nature Cancer (PMID: 35221336).

  Study phs002479

• NHLBI TOPMed: Stanford Cardiovascular Institute iPSC Biobank Study (SCVI)

  The proposed Stanford Cardiovascular Institute (SCVI) Biorepository will curate and manage an expanded collection of human induced pluripotent stem cell (iPSC) lines and provide investigators with iPSC materials generated using standardized protocols, with the overall objective of promoting the continued adoption and development of iPSC technology in cardiovascular research. Human iPSCs have revolutionized disease modeling, drug screening, and therapeutic research. However, it is also recognized that the need for specialized technical expertise and the associated cost have largely prevented individual research laboratories from adopting iPSC models in their inquiries, particularly in studies requiring multiple cell lines. To address this bottleneck, the proposed Biorepository will maintain our existing collection of iPSC lines and further expand the collection of iPSCs by recruiting 1,000 healthy, hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM) donors of both sexes and diverse racial/ethnic backgrounds (African Americans, Asians, Hispanics, and Whites).

  Study phs002338

• Genome-wide cell-free DNA biological patterns in patients with cancer

  The structure of cell-free DNA (cfDNA) is altered in the blood of cancer patients. From whole genome sequencing we retrieved the cfDNA fragment-end composition using a new software (FrEIA), as well as the cfDNA size and tumor fraction in three independent cohorts (n=925 cancer from >10 types and 321 control samples). At 95% specificity, we detect 72% of cancer samples using at least one cfDNA measure, including 64% of early-stage cancer (n=220). cfDNA detection correlates with a shorter overall (p=0.018) and recurrence-free (p=0.006) survival in patients with resectable esophageal adenocarcinoma. Integrating cfDNA measures with machine learning in an independent test set (n=396 cancer, 90 controls) achieve a detection accuracy of 82% and AUROC of 96%. In conclusion, harnessing the biological features of cfDNA can improve at no-extra cost the diagnostic performance of liquid biopsies.

  Study EGAS00001007400

• Genomic profiling of patient-derived xenograft models of myxoid liposarcoma either sensitive or resistant to trabectedin

  The dataset consists of two patient-derived xenograft model of myxoid liposarcoma one sensitive and one resistant to trabectedin. Both models underwent the same treatment schedule with trabectedin (tree time points and one treatment with doxorubicin). We performed genomic profiling using Agilent OneSeq assay.

  Dataset EGAD00001005099

• Human four week embryo head as reference for generating an enhancer compendium for neuronal and neural crest development using neural tube organoids.

  This study has the aim of generating an enhancer code compendium of early human neuronal and neural crest development. For this purpose, we generated human neural tube organoids from single cells from two induced pluripotent stem cell lines. The organoids were subject to combined single cell multiomics at four time points of differentiation. To evaluate the biological relevance of the cell types and states obtained from the organoids, we compared with data obtained from 10XGenomics single cell multiomics on the head of a single four weeks post conception human embryo.

  Study EGAS50000001031

• SCI-MAP: Single Cell Microgel embedded iPS-cells to map molecular variability of cell differentiation using a systems biology approach.

  In the SCI-MAP project we will map cell states encountered across a previously established 49 day in vitro chondrogenic differentiation protocol. We do this to optimise the differentiation process for therapeutic and in vitro modelling ends. We collect epigenetic open chromatin and phenotypic transcriptome data to determine cell states and so performed single nucleus sequencing in two modalities: RNA- and ATAC-sequencing. Data was collected in a time series experiment at 7 points: Days 0, 3, 6, 8, 14, 21, and 49, starting with the first pilot data from day 21 (D21).

  Study EGAS50000001041

• B cell activation

  To investigate the gene programs involved in B cell activation and antibody switching, we profiled the gene expression at the single cell level as well as the antibody repertoire of human naive and memory B cells at resting and following three time points of activation. Through CRISPR perturbations, we defined IRF4 as a central regulator of both GC and plasma cell fates, acting independently of PRDM1 in GC commitment. Finally, leveraging machine learning classification methods trained solely on transcriptomic profiles, we accurately predicted sister cell relationships, revealing that plasma cell gene expression programs are heritable and tightly conserved within a clone.

  Study EGAS50000001468

• Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies

  To identify early driver mutations in ovarian cancer cells, we used dense whole genome sequencing of micrometastases and microscopic residual disease collected at three time points from a single patient during treatment for high-grade serous ovarian cancer (HGSOC). Laser capture microdissection of tumour islets was performed on samples prior to chemotherapy, after three cycles of chemotherapy and at recurrence. Long frament read whole genome sequencing was performed and mutations were identified. To our knowledge, this is the first longitudinal study that attempts to investigate spatial and temporal micro-heterogeneity in cancer.

  Study EGAS00001001909

• Neuroblastoma_MP-PCR_MultiplexPCR_TargetedSequencing_BAMs

  This dataset contains raw sequencing data (BAM/BAI files) generated from human neuroblastoma patient samples. The data were produced using targeted high-throughput next-generation sequencing and are intended to support genomic analyses of tumor-associated alterations. All files are provided under controlled access in accordance with EGA data protection requirements.

  Dataset EGAD50000002260

• Verification of BCR reconstruction from single-cell RNA-seq using BraCeR

  This dataset was made to verify the computational reconstruction of B cell reseptors from single-cell RNA-seq using BraCeR. The dataset contains BCR-derived reads from single-cell RNA-seq from 13 cells using the Smart-seq2 protocol, as well as targeted BCR-sequencing data from the same cells.

  Dataset EGAD00001004199