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• EED inhibition of organoid development

  Transcriptomics and epigenomics after chemical inhibition of EED during early human brain organoid development. To investigate the role of H3K27me3 inhibition during neuroectoderm induction, we treated brain organoids with 3 concentrations of EED inhibitor (and control) during the transition of pluripotency to neuroepithelium. At the neuroepithelium stage, we profiled the organoids using scRNA-seq (transcriptome) and bulk Cut&Tag (H3K27me3, H3K27ac). Library preparation for scRNA-seq was carried out with the 10x genomics platform.

  Dataset EGAD50000000224

• Sex Differences in MAGEL2 Gene Promoter Methylation in High Functioning Autism - Trends from a Pilot Study Using Nanopore Cas9 Targeted Long Read Sequencing

  Using DNA extracted from peripheral blood, Cas9-targeted nanopore DNA sequencing was used to analyze MAGEL2 gene, including its entire regulatory construct (chr15:23639316-23651466), for sequence variation and 5-methyl-cytosine (5mC) modification in a cohort of adults with HFA compared to sex- and age-matched NC.

  Dataset EGAD50000000726

• RNAseq of pre- and post-5AZA-treated head and neck cancer patients refractory to anti-PD-1 therapy

  RNA sequencing (RNA-seq) was performed on baseline (before low-dose 5-aza treatment) and on-treatment (low-dose 5-aza treatment for 5 or 10 days) tumor samples from eight participants with head and neck cancer who were refractory to anti-PD-1 therapy. RNA library preparations, sequencing reactions, and initial bioinformatics analyses were conducted at GENEWIZ, LLC. In total, 16 150-bp pair-end RNAseq data were generated.

  Dataset EGAD50000001010

• Comprehensive survey for the construction of an integrated database of food, gut microbiome, and health information (the "Sukoyaka Health Survey")

  We conducted a cohort-based study to investigate the association between the genetic background and diet/lifestyle in 59 healthy Japanese. We analyzed some participants living in Nagasaki. Shotgun metagenomic sequencing of fecal microbiome were analyzed.

  Study JGAS000681

• PHRT longitudinal ovarian cancer dataset

  High-grade serous ovarian cancer presents significant challenges due to its poor prognosis and high heterogeneity, both of which complicate treatment responses. This project aims to understand intra-patient tumor evolution by investigating different sampling sites (primary and metastatic) at the time of diagnosis and during disease recurrence. A total of 183 biopsies from 50 patients were collected for this purpose, and bulk mRNA sequencing was performed. The majority of samples originated from following tissue types: omentum, ovary, and ascites.

  Dataset EGAD50000002064

• Single-cell RNA sequencing of Small Intestinal Neuroendocrine Tumors (SI-NET)

  Single-cell RNA sequencing (scRNA-seq) was performed on cells isolated from intestinal mucosa and small intestinal neuroendocrine tumors (SI-NETs) to compare their transcriptomic profiles. Tumor and adjacent normal tissues were collected from two SI-NET patients, enzymatically dissociated, and processed into single-cell suspensions. Single-cell libraries were generated using the Chromium Single Cell 3′ Reagent Kit v3 and sequenced on an Illumina platform to produce FASTQ files for downstream analysis.

  Dataset EGAD50000002265

• Somatic copy number alterations profiling in non-small cell lung cancer and their correlation with clinical efficacy in first-line treatment

  Genomic data from FFPE tumor samples of 258 patients with non-small cell lung cancer (NSCLC), profiled by shallow whole-genome sequencing (sWGS) at 1x. The study aimed to characterize somatic copy number alterations (SCNAs) and SCNA burden to assess their clinical relevance for patient stratification across different first-line treatments.

  Dataset EGAD50000002322

• Whole exome sequencing of an alveolar rhabdomyosarcoma patient with RET germline mutation

  Whole exome sequencing of an alveolar rhabdomyosarcoma patient with RET germline mutation and subsequent analysis of potential therapeutic mechanisms associated with the patient's rare germline mutation. Patient sampels were sequenced from an initial biopsy and from a relapse biopsy, in addition to normal blood as the matched normal DNA. RNA sequencing was performed on the relapse sample as initial sample was unable to produce usable RNA for analysis.

  Dataset EGAD00001006125

• The Xq22.3 contiguous gene deletion syndrome (ATS-ID): from genotype to further delineation of the phenotype

  Approximately 200 ng of high-quality of genomic DNA samples were used for library preparation. DNA libraries were prepared using the Human Core Exome Kit according to manufacturer’s recommendations (Twist Bioscience, San Francisco, CA, USA) and then sequenced on Illumina NovaSeq 6000 (Illumina, Inc., san Diego, CA, USA). Detailed protocol of WES data processing and variant analysis are available in Supplementary data.

  Dataset EGAD00001007740

• Whole genome sequencing of multifocal ileal neuroendocrine tumors

  This dataset includes whole genome sequences of 75 synchronous primary tumors, 15 metastases, and corresponding normal samples from 13 patients with multifocal ileal neuroendocrine tumors. The whole genomes were sequenced on Illumina HiSeq X Ten to generate 151-bp paired-end reads, which were aligned to GRCh38/hg38 reference assembly using BWA–MEM and duplicate-marked with Picard tools. GATK was utilized for base score recalibration and local indel re-alignments. The whole genomes are provided as CRAM files.

  Dataset EGAD00001008831