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• EASI-Genomics GM21886 Cell Line High Molecular Weight DNA Sequencing

  An interlaboratory study was performed with GM21886 cells to evaluate methods for high molecular weight (HMW) genomic DNA extraction and compare sample and sequencing QC metrics, and pipelines for structural variant (SV) calling. Four laboratories prepared HMW genomic DNA using four alternative extraction methods FireMonkey (Revolugen), Genomic Tip (QIAGEN), Nanobind (Circulomics), and Puregene (QIAGEN), followed by Short Read Elimination (Circulomics) and long-read sequencing with MinION and PromethION flowcells (Oxford Nanopore Technologies).

  Study phs003958

• MOSAIC Window DLBCL Data

  This dataset will include Spatial Transcriptomics from the 10x Genomics Visium SD technology, Single-Cell RNA-Seq from the 10x Genomics Chromium Flex protocol, Bulk RNA-Seq (sequenced on Illumina), WES (sequenced on Illumina), H&E, and Clinical data from 10 DLBCL patients. For Visium and Chromium data we are sharing the outputs of respectively Space Ranger and Cell Ranger. For Bulk RNA-Seq we are including processed files such as counts.tsv, FPKM.tsv, fusion_genes.tsv, TPM count matrix.tsv, DESeq2 count matrix.tsv, multiqc_report. For WES, we are sharing the presence or absence of single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variants (CNVs).* Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001702

• MOSAIC Window Ovarian Data

  This dataset will include Spatial Transcriptomics from the 10x Genomics Visium SD technology, Single-Cell RNA-Seq from the 10x Genomics Chromium Flex protocol, Bulk RNA-Seq (sequenced on Illumina), WES (sequenced on Illumina), H&E, and Clinical data from 15 Ovarian patients. For Visium and Chromium data we are sharing the outputs of respectively Space Ranger and Cell Ranger. For Bulk RNA-Seq we are including processed files such as counts.tsv, FPKM.tsv, fusion_genes.tsv, TPM count matrix.tsv, DESeq2 count matrix.tsv, multiqc_report. For WES, we are sharing the presence or absence of single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variants (CNVs).* Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001704

• MOSAIC Window Mesothelioma Data

  This dataset will include Spatial Transcriptomics from the 10x Genomics Visium SD technology, Single-Cell RNA-Seq from the 10x Genomics Chromium Flex protocol, Bulk RNA-Seq (sequenced on Illumina), WES (sequenced on Illumina), H&E, and Clinical data from 10 Mesothelioma patients. For Visium and Chromium data we are sharing the outputs of respectively Space Ranger and Cell Ranger. For Bulk RNA-Seq we are including processed files such as counts.tsv, FPKM.tsv, fusion_genes.tsv, TPM count matrix.tsv, DESeq2 count matrix.tsv, multiqc_report. For WES, we are sharing the presence or absence of single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variants (CNVs).* Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001706

• Bulk and Single-Nuclei RNA-seq with ATAC-seq of Breast Tumors Pre- and Post-Palbo ciclib/Endocrine Therapy

  This dataset comprises bulk and single-nuclei multiomic profiles from patients with ER+/HER2- early breast cancer enrolled in the NeoRHEA phase 2 trial. The bulk RNA-seq component includes 78 pre-treatment and 49 post-treatment tumor samples from 97 patients. The single-nuclei component includes matched pre- and post-treatment samples from 37 patients, totaling 63 samples analyzed by simultaneous snRNA-seq and snATAC-seq. Combined, the data contains bulk transcriptional profiles and single-nuclei gene expression/chromatin accessibility matrices for over 226,000 high-quality nuclei, encompassing tumor, immune, and stromal cells. Technologies used include Illumina NovaSeq 6000 for sequencing and the 10x Genomics Chromium platform (Multiome kit for single-nuclei, standard RNA library prep for bulk).

  Dataset EGAD50000002038

• RNAseq of medulloblastoma data (MB_COMICS cohort)

  Medulloblastoma (MB) is the most common malignant brain tumor in children. It is a neuroectodermal tumor located in the cerebellum. International consensus recognizes four distinct subgroups of MBs including Wingless (WNT), Sonic Hedgehog (SHH), Group 3 (G3), and Group 4 (G4) with distinct molecular characteristics, prognoses, and mortality rates in patients. Here, we have compiled and evaluated a large international MB cohort for which we generated transcriptomic data (RNAseq) for 208 primary MB patient samples.

  Study EGAS50000000410

• Influence of pre-analytical processing on blood protein profiles (AMED-Metabolites)

  The purpose of the present study was to assess the differences between the human serum and plasma proteomes, and the stability of human plasma proteins under different storage conditions following blood collection, by means of SWATH-MS analysis. We compared plasma samples prepared by centrifugation after storage of blood at room temperature for 0, 15 or 30 minutes, or under refrigeration at 0-5?C for 1, 4 or 8 hours.

  Study JGAS000223

• Comprehensive biomarker analysis from phase II study of nivolumab in patients with thymic carcinoma

  In a phase II trial of nivolumab in advanced thymic carcinoma (UMIN000022007), long SD (SD for more than 24 weeks) was seen in three patients and irAE (Gr2 or higher) was seen in four patients among 15 patients. We conducted preplanned comprehensive biomarker analyses. We obtained whole blood for Immuno Pharmacogenomic analysis using PBMC DNA. Immuno-PGx analysis showed non-synonymous SNVs in ITGAX and PDCD1 had some correlation with PFS.

  Study JGAS000588

• Bone morphogenetic protein-9 controls pulmonary vascular growth and remodeling

  Human PMECs from 10 donor lungs were isolated, cultured (passages 3 to 4), synchronized by serum starvation (0.3% FCS), and stimulated with 10 ng/mL BMP-9 for 4 h. Single-cell profiling was performed using the 10X Genomics Chromium RNA 3' V3.1 kit. Five experimental groups were analyzed using cell hashing and sequenced on an Illumina NextSeq500. Data were processed with Cell Ranger and Seurat for differential gene expression and functional enrichment analysis.

  Study EGAS50000001026

• Exome_sequencing_of_a_cohort_of_Rett_syndromelike_patients

  The aim of the project is the definition of the molecular defect in a cohort of Rett-like patients negative for mutations in known disease genes. To this aim, a number of unrelated trios (patients plus parents) will be analysed by exome sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002059