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• EDi016-C / SAMEA4768168 WGS data

  The iPSC line EDi016-C / SAMEA4768168 has undergone whole genome sequencing. Whole genome sequencing was done using Illumina HiSeq X Five platform with a reference genome of GRCh38. Raw data as FASTQ files and analysed data as CRAM files are available for this sample, in this dataset. The iPSC line EDi016-C is available for research use at www.EBiSC.org.

  Dataset EGAD50000001090

• EDi019-B / SAMEA4776418 WGS data

  The iPSC line EDi019-B / SAMEA4776418 has undergone whole genome sequencing. Whole genome sequencing was done using Illumina HiSeq X Five platform with a reference genome of GRCh38. Raw data as FASTQ files and analysed data as CRAM files are available for this sample, in this dataset. The iPSC line EDi019-B is available for research use at www.EBiSC.org.

  Dataset EGAD50000001091

• UKKi019-B / SAMEA17626168 WGS data

  The iPSC line UKKi019-B / SAMEA17626168 has undergone whole genome sequencing. Whole genome sequencing was done using Illumina HiSeq X Five platform with a reference genome of GRCh38. Raw data as FASTQ files and analysed data as CRAM files are available for this sample, in this dataset. The iPSC line UKKi019-B is available for research use at www.EBiSC.org.

  Dataset EGAD50000001096

• SGCC TMA cohort

  This Tissue Microarray (TMA) GeoMx Digital Spatial Profiler (DSP) dataset was a part of the validation cohort in the study. Tumor tissue blocks were first annotated as tumor core or tumor edge by pathologists, then Regions of Interest (ROIs) were selected on various blocks. The data is in FASTQ format. GeoMx DSP data from 840 ROIs (after QC) from 86 GCs were included in the datasets.

  Dataset EGAD50000000903

• Single-cell RNA sequencing of 16 NPM1 mutated AML patients

  This dataset contains paired-end fastq files for single-cell RNA-seq of 16 NPM1 mutated AML patients. 19 fastq pairs are included, with two samples split into two lanes and a second (technical) replicate for one patient. Libraries were constructed using 10x Genomics Chromium Next GEM Single cell 3’ v3.1 and sequencing was performed using Illumina NovaSeq6000.

  Dataset EGAD50000000478

• 10X Genomics single-nuclei RNA-sequencing of endometrium from women with and without PCOS

  Chromium Next GEM Single Cell 3’ Gel Bead Kit (Dual Index) v3.1 (10X Genomics) of endometrium from 27 women including 5 without PCOS and 12 with PCOS. Following baseline biopsies, PCOS participants underwent a 16-week randomized controlled trial with metformin (n=7) or lifestyle intervention (n=3). 25,000 raw reads per nucleus

  Dataset EGAD50000001017

• Long read sequencing to detect structural variants in Indian patient with non-syndromic autism spectrum disorders

  This study involved performing long read whole genome sequencing using Oxford Nanopore Technology platform on to detect causative structural variants in patients with non-syndromic autism spectrum disorder. This study was performed on 23 such children in whom prior karyotyping, Fragile-X analysis (in males), chromosomal microarray and whole exome sequencing did not identify a causative variant.

  Dataset EGAD50000001231

• A non-canonical lymphoblast in refractory childhood T-cell leukaemia

  Single cell mRNAseq of T-ALL samples including presentation samples for 13 with refractory disease and 8 with responsive disease, and Day 28 samples for 8 patients with refractory disease. Also includes bulk mRNA sequencing on 6 of the patients with responsive disease.

  Dataset EGAD50000001128

• Whole genome sequencing of circulating cell-free DNA on Illumina and Ultima platforms

  The dataset includes Illumina (n=1) and Ultima (n=92) sequencing of circulating cell-free DNA. The dataset was generated through standard whole genome sequencing (Illumina n=1 & Ultima n = 15) and using a duplex unique molecular identifier whole genome sequencing workflow (Ultima, n=77). This dataset includes cancer samples and cancer-free control samples.

  Dataset EGAD50000001234

• RNASeq profiles from Indian HFrEF Cohort

  The dataset contains whole transcriptomics profiling from a cohort of 49 HFrEF patients. The myocardium samples were collected from these patients during heart transplant of LVAD implantation procedure. The RNA samples were collected in RNAlater. Total transcriptome libraries were prepared using TruSeq Stranded Total RNA Library Prep with Ribo-Zero Gold kit and sequenced on Illumina HiSeq4000.

  Dataset EGAD50000001196

• Purified vs unpurified stem cell-islets

  A scRNAseq dataset consisting of stem cell-derived islets treated with gradient separation (HUES8_Pure_Islets) and unpurified control (HUES8_control_islets). scRNAseq was done on cryopreserved stage 7 stem cell (HUES8 cell line)-derived islets. Details about stem cell differentiation and sequencing can be found on the publication by Rajaei et al. (2025, Science Translational Medicine). This dataset correspond to Fig 4 of the publication.

  Dataset EGAD50000001396

• Novel genome editing strategies to uncover genotype-phenotype correlations in Polycystic Kidney Disease: a proof-of-concept

  Bulk RNA-seq of genome-edited HEK293T cell lines engineered to model specific PKD1 variants. This dataset enables the exploration of genotype-phenotype correlations in Polycystic Kidney Disease (PKD)

  Study EGAS50000001188

• Characterizing Immune Profiles in Extrapulmonary Tuberculosis via RNA Sequencing

  This dataset provides insight into the immune response in extrapulmonary tuberculosis (EPTB), using bulk RNA-seq data to analyze different disease severities. Hierarchical clustering identified three distinct levels of severity, revealing disease progression driven by interferon and IL-1β-mediated signaling. Additionally, the dataset helped develop a diagnostic gene expression signature for both EPTB and pulmonary TB.

  Dataset EGAD50000000943

• Longitudinal RNA-seq (whole blood) in a twin cohort

  The dataset consists of 232 RNA-seq samples (whole blood) obtained from healthy female from the TwinsUK adult registry cohort. The samples were obtained at two time points separated on average by 22 months.

  Study EGAS00001001763

• Thirty cutaneous SCC WES tumour samples with matched normal

  Thirty cutaneous SCC WES tumour samples with matched normal include 20 samples from South et al. JID and 10 new samples. These 30 samples has been used to support the findings in the TGFb Nature Communications paper (DOI: 10.1038/ncomms12493). They are also a part of the ongoing study of cSCC genomic landscape of 40 cSCC samples in total.

  Dataset EGAD00001002253

• De novo mutations in cell-free foetal DNA - Pulldown experiment

  A pulldown experiment with Agilent SureSelect probes designed on regions that were more likely to contain de novo mutations. 266 candidate sites were selected based on whole genome sequencing data. The probes also included the exons of genes that have been identified as neurodevelopmental disorder genes in DDD (the DDG2P genes) 1,336 targets. In addition, the design included the standard iPLEX sites.

  Dataset EGAD00001002265

• WGS dataset for Unraveling mutagenic processes influencing the tumor mutational patterns of individuals with Constitutional Mismatch Repair Deficiency

  Molecular characterization of 41 tumors from 17 individuals with CMMRD to gain a better understandig of mutational processes driving subsequent tumor development. The molecular characterization includes the investigation of tumor mutational load and mutational signatures.

  Dataset EGAD00001015157

• Glioblastoma CRISPR Screen (2016-06-02)

  This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs. This dataset contains all the data available for this study on 2016-06-02.

  Dataset EGAD00001002158

• Single Cell Targeted DNA sequencing for Variant Calling in T-ALL

  This dataset contains the raw fastq-files and the VCF files of single cell targeted DNA sequening with the MissionBio Tapestri platform. This was performed on 8 male pediatric T-ALL cases: X09-XB37-XB47-XD83-XF91-XF97-XF100-XF121. For some patients we have timepoints during treatment: XF100 and XG121. XD83 is a patient that relapsed twice.

  Dataset EGAD00001006167

• RNA-sequencing of a normal CD34+ cells

  Sample libraries were prepped using 500 ng of input RNA according to the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Amplified sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina) and aligned against the human genome (hg19) using STAR v2.5.4b2.

  Dataset EGAD00001007646

• Whole Genome Sequencing of INTERVAL (2019-06-12)

  15x Whole Genome Sequencing of 15,000 individuals from the INTERVAL study cohort, phase II. 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/ . This dataset contains all the data available for this study on 2019-06-12.

  Dataset EGAD00001005085

• Metadata and count matrix

  The dataset contains metadata for all cells before scRNA-seq quality control and for cells passing quality control. It also contains a count matrix with Salmon gene counts for all cells passing quality control, and reconstructed B-cell receptor sequences using the computational tool BraCeR. The scRNA-seq data was generated using the Smart-seq2 protocol and sequenced on Illumina NextSeq500.

  Dataset EGAD00001006435

• Targeted amplicon sequencing on 218 samples from Stage 1 epithelial ovarian cancer biopises

  BAM files (aligned against the hg38 genome) from a targeted amplicon sequencing (139 genes) experiment (median depth 1000X) on 218 samples from Stage 1 epithelial ovarian cancer biopises. Samples labeled "bis" or "tris" with the same ID are relapses; "left" or "right" samples indicate, in the case of bilateral tumor, from which ovary the sample was taken.

  Dataset EGAD00001006873

• CNV detection in targeted NGS panel data

  We present targeted NGS panel data from 170 samples that were processed using the TruSightTM Cancer (TSC) panel (Illumina, San Diego, CA, USA), which targets 94 genes and 284 SNPs associated with a predisposition towards cancer. The samples are enriched for CNVs in the genes of interest. All CNVs have previously been assessed with MLPA and can therefore be considered as confirmed.

  Dataset EGAD00001003400

• CGH Array

  DNA samples were extracted from peripheral blood lymphocytes using commercially available kit (Puregene Core Kit A, Qiagen) according to manufacturer's protocol. Agilent SurePrint G3 Human CGH Microarray 180K platform was used for screening of copy number aberrations (CNAs) using array-CGH protocol recommended by manufacturer (Agilent Technologies), data mining and interpretation of array-CGH results was performed in same manner as in our previously published results.

  Dataset EGAD00001007743