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• DNA Double Strand Breaks in KMT2A-Rearranged AML patients

  DNA breakage at specific rearrangement-participating genes, which are more sensitive to a range of environmental and chemotherapeutic agents than other regions of the human genome, contributes to the generation of leukemia-causing rearrangements, and can be used as a predictor of susceptibility to cancer caused by gene rearrangements. As a direct proof-of-principle regarding the feasibility of employing fragile site breakage to identify and monitor high-risk populations to allow personalized treatments, genome-wide DNA break mapping/sequencing was used to determine whether preferential DNA breaks are generated at the major breakpoint regions of KMT2A in AML remission patients with previously diagnosed KMT2A rearrangement. We are submitting break mapping data from three patients with KMT2A rearrangements and three non-fusion patients, with and without etoposide treatments.

  Study phs002804

• 3.5KJPNv2, an allele frequency panel of 3,552 Japanese individuals

  In the Tohoku Medical Megabank Project, we have conducted whole-genome sequencing of nearly 4,000 individuals from a Japanese population, and constructed an allele frequency panel of 3,552 individuals (3.5KJPNv2) after removing genetically related individuals. The 3.5KJPNv2 was constructed by using a standard pipeline including the 1KGP and gnomAD algorithms to reduce technical biases and to allow comparisons to other populations. The 3.5KJPNv2 includes variants in chromosome X and mitochondrial genome as well as autosome. The submitter has changed the access level of this study from controlled-access [Type I] to un-restricted access since 11th, January, 2019. The un-restricted access data ?hum0015.v3.3.5kjpnv2.v1? are available at the NBDC site: https://humandbs.biosciencedbc.jp/en/hum0015-v3. This study does not contain any controlled-access dataset.

  Study JGAS000159

• 10x genomics single cell RNA-seq and ATAC-seq from 10 pre-menopausal patients fimbriae and ampullary part of the fallopian tube

  The fallopian tube, connecting the uterus with the ovary, is a dynamic organ that undergoes cyclical changes and is the site of several diseases, including serous cancer. Here, we use single-cell technologies to construct a comprehensive cell map of healthy pre-menopausal fallopian tubes, capturing the impact of the menstrual cycle and menopause on different fallopian tube cells at the molecular level. The comparative analysis between pre- and post-menopausal fallopian tubes reveals substantial shifts in cellular abundance and gene expression patterns, highlighting the physiological changes associated with menopause. Further investigations into menstrual cycle phases illuminate distinct molecular states in secretory epithelial cells caused by hormonal fluctuations. The markers we identified characterizing secretory epithelial cells provide a valuable tool for classifying ovarian cancer subtypes.

  Study EGAS50000000628

• SCA1 and control cerebral organoids

  3' RNA-sequencing data of cerebral organoids from controls and individuals with SCA1 was performed at day 31 and day 60 of organoid formation. Matched case-control cerebral organoids were used (Ctrl A+SCA1 A and Ctrl B+SCA1 B) as well as isogenic cerebral organoids, CRISPR/Cas9 gene-edited from Ctrl A (SCA1-/CAG and SCA1CAG/CAG). Biological triplicates were assessed for all lines at both time points.

  Dataset EGAD50000002473

• High-depth whole genome sequencing of clonal colorectal cancer PDX-derived organoids and xenografts

  High-depth WGS was performed on two clonal organoids, one ancestor and one endpoint of a single lineage in a mutation accumulation experiment, and of the same clonal organoid that has been engrafted and grown in xenografts during the accumulation period. Paired sequencing was performed on a Novaseq X Plus with 150bp reads aiming at 500Gbp - 150x. 6 fastq files have been deposited for the 3 samples

  Dataset EGAD50000002528

• Spatial CosMx Human 6K

  we profiled the cellular composition and TME spatial organization in 4 ICB-resistant HCC patients using single-cell spatial transcriptomics (CosMx Human 6K Discovery Panel). We identified 397 fields-of-view (0.51 mm by 0.51 mm) of hematoxylin and eosin (H&E)-defined tumor and stromal regions followed by cell segmentation using a nuclear stain plus 4 protein markers, yielding 485,209 high-confidence single-cell profiles that were subsequently categorized into distinct cell types based on marker gene annotation.

  Dataset EGAD50000002052

• M116 Whole Genome Sequencing

  Whole Genome Sequencing (WGS) was performed using DNA extracted from M116’s blood, saliva, and urine samples. DNA was fragmented to 350 bp, followed by library preparation, paired-end 150 bp WGS, and variant calling, all conducted by Novogene®. Sequencing was carried out with a 10X coverage (approximately 60 Gb and 200 million reads per sample) using the NovaSeq X Plus platform (Illumina). Files types included in this dataset are raw Fastq files.

  Dataset EGAD50000001286

• RNA fastq files and mutation annotation files

  This dataset contains the results of both RNA sequencing and DNA sequencing. For RNA sequencing, it includes data from 12 samples derived from 9 patients, provided as raw sequencing files in FASTQ format. For DNA sequencing, it contains mutation information obtained from targeted panel DNA sequencing, including data from 35 individuals in the mutation annotation file (MAF) format.

  Dataset EGAD50000001768

• Transcriptome profiling of head and neck squamous cell carcinomas with paired patient-derived xenografts

  This dataset includes transcriptome profiling of 88 head and neck primary patient tumor samples and 45 paired patient-derived xenograft samples that successfully engrafted in mice. NGS was performed using the Illumina TruSeq stranded total RNA sample preparation kit on the Illumina NovaSeq X Plus platform at the Princess Margaret Genomics Centre. This dataset consists of paired-end fastq files.

  Dataset EGAD50000000995

• SNP array

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed.
This dataset contains SNP array data for tumor/normal pairs for a subset of 36 patients from the screening cohort plus an additional relapse tumor of one of those 36 patients. Data was generated on a OmniExpress-24 v1.1 Bead Array (Illumina) and is stored in IDAT file format.

  Dataset EGAD00010002597