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• Aberrant (pro)renin receptor expression induces genomic instability by chromatin remodeler SMARCA5 disruption during the pancreatic ductal adenocarcinoma

  The aim of the present study is to elucidate whether aberrant (P)RR expression induces genomic instability in human pancreatic ductal epithelial (HPDE) cells, which are transforming into pancreatic ductal adenocarcinoma (PDAC).

  Study JGAS000143

• Immunoglobulin Heavy-Chain locus in Multiple Sclerosis (n=4)

  Peripheral-blood or monocyte DNA from two healthy donors and two individuals with multiple sclerosis were sequenced on a PromethION-2 Solo (P2 Solo) instrument using R10.4.1 flow-cells and the Ultra-Long DNA Sequencing Kit (SQK-ULK114). For each participant we provide FASTQ reads (on-target), and haplotype-resolved assemblies of the complete IGH locus (~1.3 Mb) in FASTA format.

  Dataset EGAD50000001517

• Somatic L1 retrotransposition mapping in high-grade serous ovarian carcinoma using LDI-PCR/Nanopore-sequencing

  Somatic L1 retrotransposition was mapped in high-grade serous carcinoma (HGSC) tumors using LDI-PCR/Nanopore-seq method. This method identifies somatic L1 insertions originating from two active L1 loci at chr22q12.1 and chrXp22.2. Multiple tumors from the same patient were utilised to understand L1-mediated intrapatient heterogeneity. Long-read data generated by LDI-Nanopore sequencing was aligned to the reference genome (GRCh38).

  Dataset EGAD50000001707

• Whole genome sequencing data from paired tumor and normal tissue in a cohort of NSCLC patients.

  WGS data for paired tumor and normal tissue from 260 patients in the TRACERx ctDNA study. The patient cohort is comprised of NSCLC patients undergoing surgical resection of their tumour. The patients were then followed up for a median of ~5 years after surgery, and serial blood samples were collected. The WGS data here was generated to inform the manufacture of custom ctDNA panels.

  Dataset EGAD50000001693

• WGS dataset for Multimodal antigenic escape to GPRC5D-targeted T-cell engagers in multiple myeloma

  We analyzed the genome of plasma cells collected from bone marrow samples or plasmocytoma from patients prior to (when available) and progression on anti-GPRC5D T cell engagers. Dataset includes tumor and matched normal WGS data aligned to GRCh38.p14 in bam format, as well as tumor small variant and CNV calls.

  Dataset EGAD50000001643

• DNA sequencing of sgRNAs in CRISPR-Cas9 screening and RNA sequencing of SF3B4-overexpressing liver organoids

  The dataset contains 18 samples. It includs 12 paired whole genome sequencing, and 2 matched short read and long read RNA sequencing of liver organoids, 2 paired RIP RNA sequencing samples. All the experiments were performed on Illumina platform with raw reads stored in fastq format or bam format.

  Dataset EGAD50000001625

• 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

• Sequencing data from the study "Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer"

  This dataset consists of 71 whole-genome samples and 47 RNA-seq samples. All WGS samples are provided in .bam format and RNA-seq samples are provided as .fq.gz (paired-end). Next-generation sequencing data on whole genomes were processed by aligning sequencing reads to a reference genome (NCBI build 37/hg19) using bwa-mem (0.7.13-r1126).

  Dataset EGAD50000001978

• Whole genome sequencing, DNA methylation, and gene expression data from gastrointestinal stromal tumor 30 patients

  We performed WGS along with genome-wide DNA methylation and gene expression analyses in 30 GIST cases to determine the genomic and epigenomic differences between KIT exon 11 557���558 deletions and other KIT exon 11 mutations.

  Study JGAS000604

• Whole exome sequencing and RNA sequencing of patient-derived pancreas neoplasm organoids

  Pancreatic cancers arise from two different precursors; intraductal papillary mucinous neoplasms (IPMN) and pancreatic intraepithelial neoplasm (PanIN), while biological differences in cancers originated from them remain obscure. Here, we analyzed their genomic and transcriptomic landscapes using patient-derived organoids.

  Study JGAS000263