22938 results for "ega"

in 36.47 milliseconds.

• 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

• metastatic uveal melanoma tumour biopsies (n=35)

  Tumour biopsies were obtained from uveal melanoma patients (n = 35) pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

  Study EGAS50000000836

• RNA-seq of 2D cell culture and 3D muscle bundles generated by primary myoblast cell lines and the human iPSCs derived from mosaic FSHD patients, respectively.

  The dataset includes the RNA-seq on the 2D cell culture of primary myoblast cell lines derived from FSHD patients and healthy donors (n=3 in each condition) and on the 3D muscle bundles generated by the human iPSCs derived from healthy and FSHD-affected cells of mosaic FSHD patients (n=3 in each condition)

  Dataset EGAD50000000717

• Genotypic data of the individuals in HPP project

  Dataset contains imputed SNP genetics data for human phenotype project https://humanphenotypeproject.org/. The samples are genotypes of 8958 individuals that underwent genetic sequencing based on buccal swab.Sequencing is performed at Neogen GeneSeek Laboratories using Illumina Novaseq at low-pass, targeting coverage levels of 0.5× and 1×. Imputation was done using loimpute-v0.1.0 over the aligned reads. Imputation is done for the autosomal chromosomes (1-22) using The 1000 Genomes phase 3 haplotypes (1KGP3) as a reference panel. The samples are provided in merged PLINK 1 binaries (.bed/.bim/.fam)

  Dataset EGAD00010002714

• Total RNA-seq of CRPC and NEPC

  This dataset contains total RNA-seq of 10 patient samples: 5 castration resistant prostate cancer (CRPC) and 5 neuroendocrine prostate cancer (NEPC). Total RNA-seq was constructed using ribosomal RNA-depleted random hexamer-primed RNA library preparation kit and sequenced on Illumina at pair-end 150bp. Total RNA-seq allows for circular RNA and mRNA analyses. Each sample was sequenced on two separate lanes, therefore, two pairs of raw fastq files (4 files in total) are provided for each sample.

  Dataset EGAD50000001312

• H3Africa AWI-Gen Phase 1 Pilot Microbiome Phenotype

  This is human phenotype data for participants in a gut microbiome study. This data was collected at the same time as the stool samples used for the microbiome component. Participants were also part of the AWI-Gen Phase 1 main study. https://www.ebi.ac.uk/ena/data/view/PRJEB40733

  Dataset EGAD00001006581

• 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

• stem cell-derived beta cells from cell lines RC9 and HUES8

  stem cell-derived beta cells differentiated using two different cell lines: HUES8 (non-clinical grade) and RC9 (clinical grade). iPSC stem cell lines were differentiated to pancreatic islets using differentiation protocol as detailed by Rajaei et al. (2025, Science Translational Medicine, accepted for publication). scRNAseq was done at stage 7 of differentiation (day 30) using 10X genomics 3' sequencing. Cells were annotated then subsetted for beta cells for downstream analysis

  Dataset EGAD50000001322

• CRISPRi/a of GATA2/NR4A2/SOX17 upon spontaneous iPSC differentiation

  Arrayed CRISPR screens, modulating the expression of key lineage TFs GATA2 (mesoderm), SOX17 (endoderm), and NR4A2 (neuroectoderm) in hiPSCs via CRISPR interference or activation over a time-course of spontaneous differentiation (days cultured in vitro: 0, 4, 12, and 18).

  Study EGAS50000000819

• Human glioblastoma single cell RNA-seq from two patient, sampled at different positions within as well as outside tumor

  We performed deep single-cell RNA sequencing of two rare glioblastoma cases where tissue could be sampled from tumor core to macroscopically normal cortex. We processed two to three replicates per sample with the 10X Genomics V3.1 kits. Deep sequencing was performed to about 100,000 reads per cell on the Illumina NovaSeq 6000 platform, resulting in a total of 37 BAM files.

  Dataset EGAD50000001500

• EGAC00001001864 - Data Access Committee Princess Maxima Center

  Dac EGAC00001001864

• 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

• Exome sequencing study of cells derived from QHJI14s04 human iPSC secondary cell stock

  Genomic abnormalities of cells used in regenerative medicine should be checked. This study evaluates variants on coding sequences of cells derived from QHJI14s04 human iPSC secondary cell stock. Here we conducted whole exome sequence of three vials from the stock.

  Study EGAS50000000934

• Colorectal cancer peritoneal metastasis

  This dataset consist of 72 samples profiled on whole exome sequencing and 94 samples profiled on whole transcriptome sequencing. The Agilent SureSelect Human All Exon v6 kit (Agilent Technologies) was used for whole exome sequencing. For RNA-seq experiments, library preparation was conducted using the Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit protocol (Illumina). Libraries were sequenced on a HiSeq4000 sequencer using the paired-end 150 bp read option. Sequences in cram format was provided.

  Dataset EGAD50000001199

• STARR-seq of ERa binding sites in MCF7 and Ishikawa cell lines

  A oligo-captured STARR-seq library was generated using as targets ERa binding regions indetified by ChIP-seq in Ishikawa (Endometrial cancer) and T47D (breast cancer) cell lines and, breast cancer primary tissues. STARR-seq assays have been performed in MCF-7 and Ishikawa cell lines. Cells have been cultured for 3 days in hormone deprivated (phenol-red free) media and stimulated for 6 hours by 10nM estradiol (E2) or DMSO (negative control).

  Dataset EGAD50000000015

• PASCAL-MID Targeted amplicon sequencing of CD34+ HSPCs (CGD)

  High-throughput amplicon sequencing were performed on CD34+ hematopoietic stem and progenitor cells (HSPCs) derived from 4 healthy donors and one unaffected heterozygous carrier of a CYBB c.252G>A variant causing X-linked granulomatous disease. Targeted genome editing were performed in the HSPCs of CYBA and CYBB genes using CRISPR-Cas9 and recombinant AAV6. To assess gene editing outcomes in CD34+ HSPCs, the targeted loci were amplified from genomic DNA and sequenced on an Illumina iSeq100.

  Dataset EGAD50000001651

• WGS Data from 42 Multi-Region Sampled IPMN-PDACs and 12 Matched Normal Samples

  This dataset contains whole genome sequencing (WGS) data from 42 IPMN-PDAC and 12 normal samples, with tumours collected from multiple regions within each tumour to capture intra-tumour heterogeneity. Tumour and matched normal samples were sequenced to study somatic mutations, structural variants, copy number alterations, mutational signatures and clonal evolution during IPMN-PDAC progression. The sequencing was performed using Illumina NovaSeq instrument with 150 bp paired-end reads.

  Dataset EGAD50000001687

• cryopreserved PBMC

  This dataset consists of 12 RNA samples derived from peripheral blood mononuclear cells (PBMCs) collected from three healthy donors. The samples cover four experimental conditions: fresh PBMCs (ID: 517210–517212), PBMCs subjected to a single freeze–thaw cycle (ID: 517213–517215), PBMCs refrozen in freezing mix (ID: 517216–517218), and PBMCs refrozen in TRIzol (ID: 517219–517221). Each sample is provided as a FASTQ file, and RNA sequencing was performed using the Illumina platform. This dataset enables the assessment of cryopreservation effects on PBMC transcriptomic profiles.

  Dataset EGAD50000001703

• Dataset of Study assessing the efficacy and safety of durvalumab plus olaparib plus fulvestrant in selected metastatic or locally advanced ER-positive, HER2-negative breast cancer patients.

  This dataset is made of 166 samples extracted from 1) FFPE blocks of the most recent biopsy (metastasis when applicable or primary tumor) of the breast tumor 2) Plasma samples and blood samples at baseline, at Day 1 Cycle2, Day 1 Cycle 3 and at progression or treatment discontinuation. Target sequencing has been perfomed using GREAT_A_v3 panel

  Dataset EGAD50000001665

• Longitudinal cfDNA methylome and fragmentome profiles in health

  This dataset contains 432 plasma cfDNA samples from healthy individuals, comprising a diurnal cohort of 16 participants and a cross-sectional cohort of 144 participants. Samples underwent capture-based target enrichment using a custom probe set covering 4,991 genomic regions, followed by targeted enzymatic methyl-sequencing on Illumina instruments in 150 bp paired-end mode. The dataset consists of raw FASTQ files generated from the sequencing runs, accompanied by a metadata file containing individual demographic details and sampling information.

  Dataset EGAD50000001721

• RNA004 Nanopore DRS of peripheral blood

  Direct RNA Sequencing offers the capability of standard transcriptomic analyses + RNA modification analysis, which holds promising applications for future clinical workflows. To this end, we tested the newly available RNA004 kit from ONT on human peripheral blood and provide orthogonal GLORI and IVT measurement for benchmarking of m6A-detection. The samples are from peripheral blood of a healthy control, taken at three different timepoints.

  Dataset EGAD50000001710

• Bulk RNA sequencing data of high-grade serous ovarian cancer samples (set 7-17)

  The dataset contains RNA sequencing data of 272 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000, MGISEQ or Hiseq X Ten. The 814 samples are fresh frozen tissue samples that have been collected from different tissues and time points before and during treatment. The files provided are paired fastq files.

  Dataset EGAD50000001370

• RNA-seq FASTQ files studied in Generation of hypoimmunogenic induced pluripotent stem cells by CRISPR-Cas9 system and detailed evaluation for clinical application

  This data set contains 12 paired fastq files (RNA-seq) from one wild-type iPS cell, two HLA-KO iPS clones and three CD14+ monocytes differentiated from them. The RNA-seq libraries were generated with Illumina TruSeq Stranded Total RNA library prep kit. The libraries were sequenced with Illumina NovaSeq 6000 in paired-end mode.

  Dataset EGAD50000001700

• WGS data for ctDNA monitoring for NSCLC in TRACERx

  Ultrasensitive circulating tumour DNA (ctDNA) detection can stratify clinical risk in early-stage non-small cell lung cancer (NSCLC). Here, we applied a whole-genome, tumour-informed approach to study ctDNA in more than 400 NSCLC of the TRACERx project

  Study EGAS50000001187

• Dynamics of checkpoint receptors in γδ T cell subsets are associated with clinical responses during anti-PD-1 immunotherapies

  scRNA-seq data from circulating gamma delta T cells derived from healthy donors and patients with stage IV melanoma that either responded or did not respond to anti-PD-1 monotherapy or anti-PD-1 and anti-CTLA-4 combination therapy. This dataset includes paired samples from these patients before and 3 months after the start of immunotherapy.

  Dataset EGAD50000001812

• WGS data for Pancreatic Cancer samples (resection cohort)

  WGS data from pancreatic cancer samples. These are part of a resected cohort from a tandem duplicator phenotype paper (Farooq et al, NPJ Precision Oncology, 2025). The dataset includes tumour and normal BAM files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=189 tumour/normal pairs).

  Dataset EGAD50000001834

• Extrachromosomal DNA-driven oncogene dosage heterogeneity determines therapy response in neuroblastoma

  Characterization of ecDNA copy number-dependent plasticity of neuroblastoma patient-derived xenograft models. Data corresponds to single-cell G&T sequencing from an untreated neuroblastoma PDX and single-cell multiome ATAC + gene expression sequencing of a SHH medulloblastoma tumor.

  Study EGAS50000001040

• Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma - RNA validation cohort

  This reposiroty contains bulk RNA data generated by Blood Cancer Research Group (Ostrava, Czech Republic) as a part of publication named "Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma" published in Hemapshere.

  Study EGAS50000001212

• Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma - WGS validation cohort

  This reposiroty contains bulk WGS data generated by Blood Cancer Research Group (Ostrava, Czech Republic) as a part of publication named "Elevated circulating tumor cells reflect high proliferation and genomic complexity in multiple myeloma" published in Hemapshere.

  Study EGAS50000001211

• Small RNA-Seq of MicroRNA's in extracellular vesicles of Ushers Syndrome patients

  Small RNA-Seq dataset of MicroRNA's found in tear extracellular vesicles (EVs) and hiPSC-derived retinal pigment epithelium (RPE) cells of Ushers Syndrome patients and control samples. 14 samples were isolated and assessed for quality before preparing libraries using the miReasy and TruSeq Small RNA Library Preparation Kit. Sequencing was performed on the Illumina NextSeq 2000 platform, generating paired end FASTQ files.

  Dataset EGAD50000001709

• Single cell data from TB patients

  The dataset comprises single-cell RNA sequencing (scRNA-seq) data derived from around 60,000 PBMCs collected from donors across different severity groups of extrapulmonary tuberculosis (EPTB) and healthy controls (3 healthy, 3 mild, 3 intermediate, 3 severe). The data include both transcriptomic and surface protein expression profiles obtained using the BD Rhapsody Single-Cell Multiomics System. Libraries were prepared for whole transcriptome analysis (WTA), AbSeq, and sample tagging, with sequencing performed on a NovaSeq 6000 system.

  Dataset EGAD50000001118

• A Novel APP p.V742L variant in a patient with ischemic small vessel disease enhances FE65 signalling

  We identified a novel variant in the APP gene associated with cerebral ischemic strokes, which is not seen before with APP variants. This results in increased affinity of APP for FE65, APP’s most important intracellular interactor that regulates gene transcription.

  Study EGAS50000001283

• Targeted proteomics for endotyping of chronic rhinosinusitis

  To identify biomarkers allowing for the distinction between different chronic rhinosinusitis patient groups and disease controls (n=20 of each DC, CRSsNP, CRSwNP and N-ERD), we use high-throughput targeted proteomics (Olink Multiplex platform) in nasal secretions and serum samples.

  Study EGAS50000000907

• 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

• ICARUS-BREAST01-ExomeSeq

  Efficacy, safety and biomarker analysis of ICARUS-BREAST01: a phase 2 Study of Patritumab Deruxtecan in patients with HR+/HER2- advanced breast cancer. Whole-exome sequencing (WES) is available for 43 tumor samples and 43 blood samples collected at entry into the trial.

  Study EGAS50000000542

• Treatment of CAR T cells with immunomodulatory metabolites

  Anti-Her2-CAR T cells produced from T cells derived from healthy human donors were treated with DMSO (control) or either of the immunomodulatory metabolites indole‐3‐carboxaldehyde (ICA), valeric acid (VA) and isovaleric acid (IVA) to assess effects on CAR T cell function.

  Study EGAS50000001386

• Dataset contains all Single cell RNAseq data of human neurons from the study Bouwen et al Nat Comm 2025

  These documents contain the patch seq data presented in the Bouwen et al Nat Comm 2025. Human brain samples were gathered during surgery, neurons were isolated using patch clamp glass pipette. Isolated cells were processed using Smartseq2 pipeline, and sequenced using an Illumina 2500. Files are formatted in fastq format. There are a total of 12 patient samples, each with 2 replication runs.

  Dataset EGAD50000001979

• Tapestri Sequencing Data of PDAC Autopsy Samples

  This dataset comprises single-cell DNA sequencing data for selected pancreatic ductal adenocarcinoma (PDAC) autopsy samples. It employs a targeted gene panel to identify single nucleotide variants (SNVs) and copy number variations (CNVs) using the Mission Bio Tapestri platform. The samples encompass primary and metastatic tissue from selected PDAC patients. This dataset includes 74 sample-level BAM files and 24 patient-level H5 files, generated by the MissionBio pipeline.

  Dataset EGAD50000001936

• Molecular profiling of HGBCL-DH-BCL2 patients treated in the HOVON-152 trial

  Using targeted sequencing and shallow whole genome sequencing for simultaneous screening of mutations, copy number alterations, and translocations, this study aims to identify genomic alterations associated with outcome in HGBCL-DH-BCL2 patients of the HOVON-152 trial.

  Study EGAS50000001453

• 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

• RNA004 Nanopore DRS of peripheral blood

  Direct RNA Sequencing offers the capability of standard transcriptomic analyses + RNA modification analysis, which holds promising applications for future clinical workflows. To this end, we tested the newly available RNA004 kit on human peripheral blood and provide orthogonal GLORI measurement for benchmarking of m6A-detection.

  Study EGAS50000001201

• Targeted sequencing data of regulatory regions in 200 Spanish ASD trios

  This dataset consists of genomic sequencing data obtained through targeted sequencing of regulatory regions ( 85,394 human cCREs from ENCODE v2, version 2, https://screenv2.wenglab.org/) in 200 ASD (Autism Spectrum Disorder) trios (father and mother unaffected and proband affected)(600 samples total). Sequencing was carried out at the Centre for Genomic Regulation (CRG), Barcelona, Spain. Uploaded files are .vcf (600 samples). The goals of our study were to detect de novo and inherited variants in ASD probands. Sequencing data were obtained in an Illumina NovaSeq6000 instrument.

  Dac EGAC50000000695

• 46 WES paired FASTQ germline/tumour samples from 23 early-onset prostate cancer donors from the Bob Champion Cancer Trust

  The dataset contains 46 samples: a germline and tumour sample from each of 23 donors. Donors are men diagnosed with prostate cancer at a young age, from the Bob Champion Cancer Trust. The data consists of 92 whole exome sequenced paired FASTQ files, compressed with bgzip. Exome sequences were enriched using Agilent SureSelect XT2 Human All Exon V5 baits, and sequenced with Illumina HiSeq 2500.

  Dataset EGAD50000002112

• Single-cell RNA sequencing of metastatic colorectal cancer patient-derived xenografts treated with cetuximab

  Tumor implantation and expansion were performed in two 6-week-old NOD/SCID mice. Once tumors reached an average volume of approximately 700 mm³, mice were randomly assigned to one of two treatment arms: vehicle (physiological saline, intraperitoneally, twice weekly) or cetuximab (20 mg/kg, intraperitoneally, twice weekly). After 1 week of treatment, mice were sacrificed, and tumors were harvested and preserved in sCelLiVE® Buffer for downstream single-cell RNA sequencing analysis.

  Dataset EGAD50000002103

• Single-cell RNA sequencing of metastatic colorectal cancer organoids treated with cetuximab

  Organoids were seeded in 12-well plates at a density of 5 × 10⁴ cells per well, embedded in 200 µL of Matrigel diluted 1:1 with culture medium, and maintained under EGF-deprived conditions. After four days of growth, organoids were either left untreated or treated with cetuximab (20 µg/mL). Following 72 hours of treatment, organoids were harvested, dissociated, and live single cells were sorted for single-cell RNA sequencing using the 10x Genomics platform.

  Dataset EGAD50000002104

• single cell RNA-seq of small cell lung cancer tumors

  This study investigated the transcriptomic profile of small cell lung cancer from 10 patients. Tumors were rapidly dissociated after the surgical procedure. Libraries were constructed using the VDJ NextGEM v1.1 10x Genomics Chromium kit. Samples were sequenced on a NextSeq 550 sequencer (Illumina).

  Study EGAS50000001400

• Human omentum cell atlas

  This dataset contains single-cell RNA sequencing data derived from freshly dissociated human omental tissue. The study investigates the transcriptomic landscape of the omentum by comparing samples from patients with benign conditions against those with ovarian cancer metastasis. To capture the heterogeneity of the metastatic niche, sampling was performed across distinct anatomical sites, including non-metastasized tissue, distant omental regions, peritumoral zones, and the tumor core. This comprehensive profiling aims to define the cellular remodeling associated with malignant transformation

  Dataset EGAD50000002110

• RRBS of 25 pleural mesothelioma samples (Single-end)

  The dataset contains RRBS data (bam files) for 25 pleural mesothelioma samples.The samples were sequenced on NovaSeq6000 (Illumina, San Diego, CA) in single-end 150bp mode. RRBS raw reads were trimmed for adaptor sequences using trim galore (v. 0.6.5) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and filtered for low-quality sequences using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High quality trimmed reads were mapped to the Human reference genome (UCSC genome assembly GRCh38/hg38) using Bismark (v. 0.22.3) with default parameters.

  Dataset EGAD50000002130

• Spatial Profiling Reveals Resistance in HER2+ Gastric Cancer

  HER2-positive gastric cancer (HER2+ GC) exhibits significant intra-tumoral heterogeneity and frequent development of resistance to HER2-targeted therapies. This study aimed to characterize the spatial tumor microenvironment (TME) and identify mechanisms of resistance to HER2 blockade including trastuzumab and trastuzumab deruxtecan (T-DXd) in HER2+ GC, with the goal of informing novel therapeutic strategies. We performed spatial transcriptomics on pre- and post-treatment samples from patients with HER2+ metastatic GC who received trastuzumab-based therapy.

  Dataset EGAD50000000898

• RNA-seq after drug perturbation of primary lymphoma samples

  3'-end low-depth RNA sequencing data from 108 patients with chronic lymphocytic leukemia and 8 patients with lymphoma. Each primary patient sample was treated in vitro with DMSO as a control and with up to ten small-molecule inhibitors (ibrutinib, duvelisib, everolimus, trametinib, nutlin-3a, I-BET762, MK2206, selinexor, compound 26, and a combination of ibrutinib and compound 26). Sequencing was performed on the Illumina HiSeq4000. The dataset contains FASTQ files.

  Dataset EGAD50000002166

• RNA Sequencing of Control and Myotonic Dystrophy Type 1 Cells During Myogenic Differentiation

  To investigate gene expression dynamics during myogenic differentiation in myotonic dystrophy type 1, RNA was collected from immortalized control, patient-derived, and CRISPR/Cas9-corrected myoblasts at proliferation (day -2) and at days 1 and 5 of differentiation. High-quality RNA was isolated and sequenced using poly(A)-enriched or rRNA-depleted protocols, yielding 100 bp paired-end reads with high coverage. A subset of samples at day 1 underwent deeper sequencing to enhance transcriptome resolution.

  Dataset EGAD50000001647

• Log2-CPM (voom)-normalised read-count matrix of the RNAseq Datasets of CLUSTER JIA pre-MTX cohort

  Samples were sequenced with NovaSeq6000 and the sequencing files were processed using the RSSnextflow workflow (https://gitlab.com/b8307038/rssnextflow). The raw read counts from all batches were combined. Analysis-ready batch-corrected read counts were generated using ComBat-seq. Read counts normalisation for DGE analysis was performed with limma-voom function (log2 CPM) as seen in the pipeline.

  Dataset EGAD50000002170

• DAC for STimage project

  The STimage Data Access Committee (DAC) oversees the access and distribution of datasets associated with the STimage project. This project focuses on the development and benchmarking of deep learning frameworks for spatial transcriptomics and digital pathology. The datasets managed by this DAC typically comprise paired histology images (H&E) and spatial gene expression data (e.g., 10x Genomics Visium) derived from human tissue samples. Our primary objective is to facilitate bona fide biomedical research while strictly protecting participant privacy and ensuring data is used in accordance with the original consent and ethical approvals.

  Dac EGAC50000000867

• 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

• 3D chromatin analysis of clear cell renal cell carcinoma using micro-C

  To investigate the 3D structure of chromatin in ccRCC, we performed micro-C on 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions

  Study EGAS50000001323

• RNAseq of organoid and fibroblast co-cultures

  The dataset includes whole transcriptome RNAseq BAM files of both organoids and fibroblast mono- and co-cultures with have been processed by Picard markdups. The experiment featured 6 fibroblast cell lines derived from 5 different early CRC biobank patients (pt10, pt12, pt15, pt19, pt22) as well as from different regions within those samples (normal tissue, core or invasive front). The organoids were generated from patient pt5 carcinoma samples.

  Dataset EGAD50000002202

• ZFHX4 is necessary for dopaminergic neuron differentiation and controls cell cycle by regulating LIN28A

  ZFHX4 as a transcription factor specifically induced during the in vitro differentiation of iPSC-derived mDANs. Depletion of ZFHX4 during neuronal differentiation led to a significant reduction in the number of mDANs while its overexpression did not lead to any changes in mDAN count. Identification of ZFHX4 target genes using CUT&Tag profiling and RNA-seq upon ZFHX4 knock-down (KD) revealed its involvement in cell cycle regulation during mDAN differentiation

  Dataset EGAD50000001605

• 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

• Using RNA-sequencing to characterize the resistance to lirafugratinib

  In addition to Exome-sequencing, we used RNA-sequencing to also characterize resistance to lirafugratinib with whole exome sequencing in patients with FGFR2-driven cancers, treated in the phase 1/2 ReFocus trial (NCT04526106) and enrolled in the UNLOCK program at Gustave Roussy

  Study EGAS50000001370

• 3D chromatin contacts of iPSC (controls) and mDAN (differentiated neurons) cells

  Sequencing of 3 replicates per condition to gather insights on the 3D chromatin conformation of iPCS-derived neuronal progenitors (smNPCs) and mDANs using LowC. The downstream analysis studies changes in A and B compartment interactions and in topologically associated domains (TADs).

  Study EGAS50000001578

• Bulk RNA sequencing of 36 multi-region IPMN–PDAC tumours comprising 160 sequencing runs

  This dataset contains bulk RNA sequencing data generated from 36 multi-region tumour samples obtained from patients with intraductal papillary mucinous neoplasms (IPMN) and associated pancreatic ductal adenocarcinoma (PDAC). A total of 160 sequencing runs are included. Libraries were prepared from poly(A)-selected RNA and sequenced on an Illumina platform. The data are provided as raw sequencing files for downstream transcriptomic analyses.

  Dataset EGAD50000002215

• Long read whole genome sequencing data from brain postmortem tissue

  Dataset consisting of 172 whole genome sequencing runs from healthy controls and Parkinson's disease patients. The data was sequenced on Oxford Nanopore (PromethION) platform. The data has been mapped to T2T-CHM13v2.0 reference genome. The data processing pipeline is available on the following link: [https://zenodo.org/records/13385065](https://zenodo.org/records/13385065). The data is in CRAM format and subet of donors also have information on C (hydroxy)methylation (MM and ML tag). The reads are also phased (HP tag).

  Dataset EGAD50000001349

• WGS data of paediatric ETV6::RUNX1 B cell acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM/CRAM files from diagnostic and matched remission (control) samples of five ETV6::RUNX1 ALL patients (ALLT-380, ALLK-114, ALLT-388, ALLT-392, ALLT-394). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), using NEBNext® Ultra™ II DNA Library Prep Kit (Cat No. E7645). Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002285

• Aligned FOS RNA sequencing data

  Total RNA-sequencing Paired-End was performed by GenomeScan (Leiden, the Netherlands) on the NovaSeq6000 platform for full-length FOS (FOS FL), truncated FOS (FOSΔ), a FOS isoform with an L376N mutation (FOS mut), untransduced fMSC (unt) and fMSC with empty pLV (pLV) at week 0, 1, 2, and 3 in triplicate (total of 60 samples). Raw RNA-seq data were processed by the RNA-seq BioWDL pipeline pipeline version 5.0.0 developed by the SASC team at LUMC, LUMC, Leiden, the Netherlands).

  Dataset EGAD50000001839

• human placenta derived trophoblast organoids expression changes by co-culturing with adipose spheroids

  This dataset includes the Prime-seq raw sequencing data of the 3 replicates of trophoblast organoids co-cultured with adipose spheroids and 3 without adipos spheorids. The libraries were generated according to the published Prime-seq library preparation protocol, and were multiplexed with all the samples from the experiment. The libraries were sequenced on Illumina NovaSeq 6000 at Novogene. The files are paired fastq files.

  Dataset EGAD50000001223

• WTCCC case-control study for Bipolar Disorder - Combined Controls

  WTCCC genome-wide case-control association study for Bipolar Disorder (BD) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000002

• Oxford Nanopore Adaptive Sampling WGS

  Eight samples were analyzed on an Oxford Nanopore MinION flow-cell, and to evaluate multiplexing, four samples were run together on one flow-cell on the P2 Solo device. Using adaptive sampling, we targeted 10 regions of different structural variant types, including deletions, translocations and complex rearrangements. MinION sequencing resulted in between 14.1-18.3 Gb of data per flow cell, with mean autosomal on-target coverage of 28.4x and off-target read depth coverage of 5.3x.

  Dataset EGAD50000001821

• DAC for "Transcriptome analysis of human iPSC-derived microglia in a novel human 3D cortical tissue model"

  scRNA-seq analysis of human iPSC-derived microglia in a novel, human in vitro 3D cortical tissue model. Samples include three distinct conditions (each as biological duplicates): wild-type microglia extracted from cultures after 1 month (WT_1mo) and 3 months (WT_3mo) of culturing, as well as knock-in microglia extracted from cultures carrying three familial AD mutations in the APP gene (Swedish, Iberian, Arctic; introduced by CRISPR/Cas9-mediated knock-in) after 3 months of culturing (KI_3mo).

  Dac EGAC50000000303

• TenK10K Phase 1: Whole Genome Sequencing SNP + indels multi-sample VCFs

  SNP and indel variants were called for 1,925 samples from phase 1 of the TenK10K project. Variant calling from WGS alignments to the GRCh38 reference assembly was performed using GATK4 HaplotypeCaller in DRAGEN mode. These VCFs consist of common (>=1% minor allele frequency [MAF]) and rare (<1% MAF) variants . This dataset is comprised of autosomal variants provided as multisample compressed VCF format files. Principal component scores were derived by using gnomAD’s run_pca_with_relateds method.

  Dataset EGAD50000002377

• Single‑nucleus multiome data of human fetal livers

  Single‑nucleus multiome data of 53 human fetal liver hematopoiesis spanning 5-18 post-conception-weeks. Nuclei were isolated after tissue dissociation and sorting live CD45+CD235- cells, and processed according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Manual specifications. Sequencing data was processed with CellRanger Arc v2.0.2 and aligned to GRCh38-2020-A-2.0.0.

  Dataset EGAD50000002337

• Precancerous lesions in Lynch Syndrome

  This dataset includes whole-exome sequencing data from precancerous colorectal lesions (adenomas and advanced adenomas) obtained from 19 patients with Lynch syndrome. Forty-four samples are analyzed, including 33 mismatch repair–deficient (dMMR) and 11 mismatch repair–proficient (pMMR) lesions as assessed by immunohistochemistry. Library preparation was performed using the Twist Human Core Exome + RefSeq + Mitochondrial Panel, followed by sequencing on the Illumina NovaSeq 6000 platform. Aligned BAM files were generated with the DRAGEN pipeline using the human reference genome hg38

  Dataset EGAD50000002222

• Genomic analysis of seminomas

  This study looks at the genomic landscape of seminomas, based on exome sequencing data and SNP array data. Eight seminoma tumors and their matched normal DNAs were exome sequenced on Illumina platforms. The same samples were also processed on Affymetrix SNP 6.0 arrays.

  Study EGAS00001000943

• HipSci_RNASEQ_Congenital_hyperinsulinia

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from Congenital hyperinsulinia patients.

  Study EGAS00001001988

• HipSci_RNASEQ_Alport

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from Alport syndrome patients.

  Study EGAS00001001986

• SNU_WGS_AML

  This study includes 10 paired samples of Korean AML paitients.10 AML tumor samples are paired with each normal(Saliva or BM derived) sequencing data.The results of this WGS study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001001906

• HipSci_RNASEQ_Battens

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from Battens patients.

  Study EGAS00001001987

• HipSci_RNASEQ_Ataxia

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from hereditary cerebral ataxia patients.

  Study EGAS00001001992

• HipSci_RNASEQ_BPD

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from Blood platelet disorders patients.

  Study EGAS00001001993

• HipSci_RNASEQ_Hypertrophic_Cardiomyopathy

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from Hypertrophic Cardiomyopathy patients.

  Study EGAS00001001994

• Resistance_to_MAPK_inhibitor_induces_internal_duplication_in_BRAF

  2 BRAFV600E cell lines that have been made resistance to 1. the BRAF inhibitor PLX4720 and 2. the combination therapy of dabrafenib and trametinib seem to have a internal duplication in the kinase domain. We would like to know if this is caused by a translocation.

  Study EGAS00001001304

• Yemen_and_Chad_Genotyping

  HumanOmni2.5-8 data from Chad and Yemen.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 EGAS00001001231

• HipSci_RNASEQ_Macular_Dystrophy

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from Macular Dystrophy patients

  Study EGAS00001001995

• Multiple_Malignancy_Familial_Comparison

  Patient (who has had multiple malignancies) has previously been found to harbour a pathogenic p53 variant which is probably mosaic. This finding is based on exome sequencing performed elsewhere. In this study we will resequence the locus in question to ascertain whether the variant is indeed mosaic.

  Study EGAS00001000333

• ORCADES_WGA

  The ORCADES Whole Genome Sequence Study plans to sequence the genomes of 400 subjects from the Orkney Complex Disease Study (ORCADES) at low coverage, each with data on up to 300 quantitative traits and other risk factors associated with cardiovascular, metabolic and other complex diseases

  Study EGAS00001000068

• WTCCC2 Reading and Mathematics (RM) samples

  A WTCCC2 project genome-wide association study for reading and mathematics ability in 3665 12-year-old individuals from the UK, genotyped on the Affymetrix 6.0 array. Details of the WTCCC2 analysis can be found in Davis et al. [Nat. Commun. 2014 July;5:4204]

  Study EGAS00001000886

• Human_Evolution_3B

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages will be sequenced using the standard whole-genome sequencing followed by filtering out autosomal and X sequences, so that only mtDNA and the Y chromosome would be analysed and released.

  Study EGAS00001000718

• Landscape of gene mutations in Down syndrome-related myeloid disorders

  To identify the spectrum of gene mutations in Down syndrome-related myeloid disorders, whole genome sequencing of 4 trio samples from TAM/AMKL/complete remission (CR) phases and whole exome sequencing of 15 TAM and 14 DS-AMKL samples were performed.

  Study EGAS00001000546

• SNU_PROSPECTIVE

  This study includes 5 paired samples of Korean AML paitients. 5 AML tumor samples are paired with each normal(Saliva or BM derived) sequencing data.The results of this WES study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001002154

• RNAseq_of_patients_with_Ewings_sarcoma

  Cancer is driven my mutations in the genome. We will uncover the mutations that give rise to Ewing’s sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewings’ sarcoma tumours.

  Study EGAS00001000267

• Ewings_Sarcoma_Rearrangement_Screen

  Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing’s sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewings’ sarcoma tumours.

  Study EGAS00001000362

• Clonal_architecture_of_pre_malignant_and_malignant_tumours

  Single cells have been isolated from normal and pre-invasive lung cancer lesions from one patient. These have been grown into colonies that will then be whole genome sequenced. This will reveal the mutational burden in normal and premalignant tissues, and the heterogeneity between different cells.

  Study EGAS00001001676

• Genetic landscape of pediatric Low Grade Gliomas & Glioneuronal tumors

  We performed whole-genome sequencing of 42 paired tumor/normal LGG genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000255

• Mutant_clone_mapping_in_normal_oesophagus

  We will use targeted exome sequencing to examine normal appearing epithelium and whole exome and whole genome sequencing of microdissected clones identified by immunostaining Some of the samples will be of low DNA concentration and therefore may require extra rounds of amplification during library prep.

  Study EGAS00001001874

• HipSci_RNASEQ_Spastic_paraplegia

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from Spastic paraplegia patients

  Study EGAS00001001991

• Breast_cancer_sequential_sampling_study

  This study aims to whole genome sequence DNA derived from breast cancer patients who received neo-adjuvany chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.

  Study EGAS00001000300

• Whole genome sequencing of metastatic melanomas from a patient with primary resistance to BRAF inhibition

  Here, we investigated the underlying cause of treatment failure in a patient with BRAF mutant melanoma who presented primary resistance. We used whole-genome sequencing (WGS) to characterise five metastatic tumours from a BRAF mutant melanoma patient who presented intrinsic resistance.

  Study EGAS00001000580

• HipSci_RNASEQ_Kabuki

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from kabuki patients

  Study EGAS00001001989

• Mutations in PNPLA6 are linked to photoreceptor degeneration and various forms of childhood blindness

  In this work, using exome sequencing, we identified biallelic PNLPA6 mutations in patients with childhood blindness due to severe photoreceptor death and clinical features of Leber congenital amaurosis (LCA) and, interestingly, also of the rare Oliver McFarlane Syndrome

  Study EGAS00001001013

• Exome_sequencing_of_patients_with_Ewings_sarcoma_

  Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing’s sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewings’ sarcoma tumours.

  Study EGAS00001000266

• Myeloproliferative_Neoplasms__MPN__Targeted_Gene_Screen

  Pulldown experiments will be performed on a number of patients with Myeloproliferative Neoplasms (MPN). The pulldown will be a bespoke design targeting known mutations, this pulldown will be sequenced and analysed to inform prevalence of mutations and to inform to the possibility of use as a diagnostic tool.

  Study EGAS00001000406