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• RNA-seq libraries from FFPE samples using Illumina Ribo-Zero Plus kit

  RNA was extracted from FFPE human tissue samples and used to prepare RNA-seq libraries with the Illumina Stranded Total RNA Prep Ligation kit with Ribo-Zero Plus. cDNA synthesis was performed starting from 100 ng of DNA-free RNA. Libraries were amplified with 16 PCR cycles and sequenced in paired-end mode (2×150 bp) on the Illumina NextSeq 550 platform. Library quality was assessed with Bioanalyzer and Qubit.

  Dataset EGAD50000001553

• MissionBio single cell DNA and protein seq for 2 samples

  This dataset contains MissionBio Targeted single-cell DNA and Protein sequencing data from a primary sample and a patient-derived xenograft (PDX) model, which is used to investigate the clonal evolution in the FOXF1/FENDRR ALL subtype. All the 2 samples are in bam file type.

  Dataset EGAD50000001793

• RNA-seq data of proliferative vitreoretinal diseases and healthy human retinal pigment epithelium

  This dataset contains RNA-seq data generated from surgical specimens of proliferative vitreoretinal diseases (including proliferative vitreoretinopathy and epiretinal membranes) and from retinal pigment epithelial cells isolated from post-mortem donor eyes. Total RNA was extracted and cDNA libraries were prepared using the Ovation Solo RNA-seq Kit (Tecan). Sequencing was performed on the Illumina NovaSeq 6000 platform. Raw FASTQ files are included to enable downstream analyses such as gene expression profiling.

  Dataset EGAD50000001780

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cardiff, UK (Owen)

  This research project was a collaboration between Cardiff University, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 1,105 Bipolar case/control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing CRAM files.

  Dataset EGAD50000001212

• WES analysis of DMD-ASD, DMD-ID and DMD-Control individuals for de novo and rare risk variants analysis

  This project generated a whole-exome sequencing (WES) dataset of 83 boys with a pathogenic variant in the DMD gene, along with WES data from the parents of 38 of them, totaling 159 samples. In addition to DMD, 12 boys also had ID (12 DMD-ID samples), 36 boys had ASD (DMD-ASD samples) and 35 did not present ID or ASD diagnosis (DMD-Control samples).

  Dataset EGAD50000001113

• WES of serrated polyposis syndrome

  Samples were obtained from patients diagnosed with serrated polyposis syndrome (SPS). To provide further detail, the dataset comprises two whole-exome sequencing samples from patients within the same family, uploaded in BAM file format with IDs 449758 and 449549. Exomic regions were sequenced using HiSeq2000 Platform (Illumina, San Diego, USA) and Sure SelectXT All Exon v5 kit (Agilent, Santa Clara, CA, USA) for exon enrichment. Only those potentially pathogenic germline genetic variants shared by both individuals were considered.

  Dataset EGAD50000001126

• High-grade serous ovarian carcinoma tumour exome sequencing variants

  Tumour variants (in VCF format) from exome sequencing (using Agilent SureSelect and TWIST library preparation systems followed by sequencing on Illumina HiSeq and NovaSeq platforms) of 108 high-grade serous ovarian tumour samples. Germline variants from EGAD00001006030 for these individuals were used to call somatic and tumour-only variants separately, creating two VCF files per sample (except for one sample without paired germline data- somatic variant file only provided). The dataset comprises 215 VCF variant files.

  Dataset EGAD50000001132

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Stockholm, Sweden (Pedersen)

  This research project was a collaboration between the Karolinska Institute BioBank and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 4,765 control samples from collaborators in Sweden. Genomic DNA from each samples was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing CRAM files.

  Dataset EGAD50000001026

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from the Netherlands (Ophoff)

  This research project was a collaboration between UCLA and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 1,965 Bipolar case/control samples from collaborators in the Netherlands and UCLA. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing CRAM files.

  Dataset EGAD50000000983

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from London, UK

  This research project was a collaboration between University College London, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 4,627 Bipolar case/control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing CRAM files.

  Dataset EGAD50000000950

• Indonesian Genome Diversity Project 3

  Low coverage whole genome sequences (1-3x) were collected to study human genetic history across Wallacea archipelago and West Papuan Region of Indonesia . We collected 254 newly sequenced genomes mostly from previously undocumented populations including 9 communities in Wallacea and 3 in West Papuan regions. Out of 254, there are 8 high coverage whole genome sequences were produce in the study (L4).

  Dataset EGAD50000000647

• 16SV4-sequence data

  Raw 16SV4-sequence data from bronchial brushing DNA obtained from healthy volunteers prior to and four weeks after ICS treatment.

  Dataset EGAD50000000527

• WES of Bipolar cases and controls performed at the Broad Inst on cohort from Cardiff, UK (Craddock)

  This research project was a collaboration between Cardiff University, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 2,458 Bipolar case/control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing CRAM files.

  Dataset EGAD50000000547

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cardiff, UK (O'Donovan)

  This research project was a collaboration between Cardiff University, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of Bipolar case/control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing CRAM files.

  Dataset EGAD50000000887

• Whole transcriptome sequencing of pheochromocytoma and paraganglioma arising from germline SDHB mutations

  Paired-end 150 basepair whole transcriptome sequencing of 91 SDHB-deficient non-metastatic and metastatic pheochromocytoma and paraganglioma. Samples were prepared using the NEB-Next directional RNA-Seq kit (NEB, USA) and underwent 150bp paired-end sequencing on the Illumina NovaSeq 6000 (Illumina, USA) according to manufacturer’s instructions. This dataset contains raw sequencing reads in FASTQ format.

  Dataset EGAD50000000504

• RNASeq profiles of ROBUST clinical trial and processed WGS mutation calls output

  The dataset contains RNAseq profiles of 1040 patients from the ROBUST clinical trial (NCT02285062). The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. RNAseq libraries (75PE, 50M) were constructed using Illumina TruSeq RNA Access method. Fastq files are included. Also includes processed WGS mutation calls output.

  Dataset EGAD50000000482

• RNAseq profiles from the CheckMate-142 clinical trial

  The dataset contains RNAseq profiles of 57 patients from the CheckMate-142 clinical trial. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. Baseline tumor tissue samples were processed using the Illumina TruSeq RNA Access in-solution hybrid capture panel and underwent subsequent NGS on the Illumina NovaSeq platform. Fastq files are included.

  Dataset EGAD50000000609

• WHOLE GENOME SEQUENCING FOR THE CHARACTERIZATION OF CLEAR CELL RENAL CELL CARCINOMA IN VHL PATIENT

  To characterize clear cell Renal Cell Carcinoma (ccRCC), we set up a comprehensive multi-omics pilot study on a VHL-ccRCC-patient. Whole Genome Sequencing (WGS) was applied on six ccRCCs, four cysts and one blood DNA sample as germinal control. Raw-data were analyzed with GENomics-DRAGEN platform. We will upload WGS-Data for 11 samples (6 ccRCCs, 4 Cysts, 1 blood).

  Dataset EGAD50000000425

• Profiling of gene expression and epigenomics in the fetal brain

  scRNA-seq and Cut&Tag from a sample of the human fetal brain. To compare neurogenesis in the primary human brain with that in organoids, we profiled transcriptome and chromatin accessibility (10X multiome) as well as bulk Cut&Tag of histone modifications H3K27me3, H3K27ac and H3K4me3. We used a human brain sample from GW 19 for all experiments.

  Dataset EGAD50000000225

• Transcriptomic analysis of LINE1 expression in the human brain

  Twist Bioscience probes were designed to LINE1 and HERV sequences for targeted amplification. Enriched cDNA libraries were then sequenced on the PacBio Sequel II, 4 samples/SMRTcell. The available files have undergone ccs (using the default parameters except for --min-rq 0.9, which was a recommended parameter for Iso-Seq) and barcode demultiplexing. Recommended analysis follows https://isoseq.how/, starting at the primer removal and demultiplexing step with lima.

  Dataset EGAD50000000265

• OAK GO28915 Source Table

  Source data of clinical study data corresponding to figures reported in the paper titled: Anti-TIGIT antibody improves PD-L1 blockade through myeloid and Treg cells. PMID: 38418879 DOI: 10.1038/s41586-024-07121-9

  Dataset EGAD50000000368

• GO30103 Source Tables

  Source data of clinical study data corresponding to figures reported in the paper titled: Anti-TIGIT antibody improves PD-L1 blockade through myeloid and Treg cells. PMID: 38418879 DOI: 10.1038/s41586-024-07121-9

  Dataset EGAD50000000367

• Cityscape Source Tables

  Source data of clinical study data corresponding to figures reported in the paper titled: Anti-TIGIT antibody improves PD-L1 blockade through myeloid and Treg cells. PMID: 38418879 DOI: 10.1038/s41586-024-07121-9

  Dataset EGAD50000000366

• Arcagen – thoracic malignancies

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting the dataset that contain NGS files from rare thoracic malignancies (n=102)

  Dataset EGAD50000000168

• Dataset for Fragle Software Development and Evaluation

  Fragle is a deep learning based two stage model that quantifies ctDNA from blood plasma derived cfDNA bam files. Fragle was developed using some previously published datasets and some newly generated data. Fragle was evaluated using some validation cohorts and some unseen cohorts. Some of these cohorts are newly created consisting of total 365 low pass (2-3X) whole genome sequencing bam files mapped to hg19/GRCh37. This dataset contains these newly generated bam files.

  Dataset EGAD50000000167