23272 results for "ega"

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• EDi012-C / SAMEA4459364 WGS data

  The iPSC line EDi012-C / SAMEA4459364 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 EDi012-C is available for research use at www.EBiSC.org.

  Dataset EGAD50000001064

• EDi013-C / SAMEA4459368 WGS data

  The iPSC line EDi013-C / SAMEA4459368 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 EDi013-C is available for research use at www.EBiSC.org.

  Dataset EGAD50000001065

• EDi015-B / SAMEA4459375 WGS data

  The iPSC line EDi015-B / SAMEA4459375 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 EDi015-B is available for research use at www.EBiSC.org.

  Dataset EGAD50000001066

• UKKi018-C / SAMEA103988380 WGS data

  The iPSC line UKKi018-C / SAMEA103988380 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 UKKi018-C is available for research use at www.EBiSC.org.

  Dataset EGAD50000001067

• RCi004-A / SAMEA3106011 WGS data

  The iPSC line RCi004-A / SAMEA3106011 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 RCi004-A is available for research use at www.EBiSC.org.

  Dataset EGAD50000001069

• RCi004-B / SAMEA3106205 WGS data

  The iPSC line RCi004-B / SAMEA3106205 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 RCi004-B is available for research use at www.EBiSC.org.

  Dataset EGAD50000001070

• RCi005-A / SAMEA3961534 WGS data

  The iPSC line RCi005-A / SAMEA3961534 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 RCi005-A is available for research use at www.EBiSC.org.

  Dataset EGAD50000001071

• RCi007-C / SAMEA4084916 WGS data

  The iPSC line RCi007-C / SAMEA4084916 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 RCi007-C is available for research use at www.EBiSC.org.

  Dataset EGAD50000001072

• UOXFi007-A / SAMEA103988274 WGS data

  The iPSC line UOXFi007-A / SAMEA103988274 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 UOXFi007-A is available for research use at www.EBiSC.org.

  Dataset EGAD50000001079

• EDi018-B / SAMEA4773418 WGS data

  The iPSC line EDi018-B / SAMEA4773418 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 EDi018-B is available for research use at www.EBiSC.org.

  Dataset EGAD50000001080

• EDi018-C / SAMEA4774168 WGS data

  The iPSC line EDi018-C / SAMEA4774168 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 EDi018-C is available for research use at www.EBiSC.org.

  Dataset EGAD50000001081

• UKKi020-C / SAMEA103988344 WGS data

  The iPSC line UKKi020-C / SAMEA103988344 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 UKKi020-C is available for research use at www.EBiSC.org.

  Dataset EGAD50000001082

• UKKi021-B / SAMEA103988346 WGS data

  The iPSC line UKKi021-B / SAMEA103988346 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 UKKi021-B is available for research use at www.EBiSC.org.

  Dataset EGAD50000001083

• UKKi022-C / SAMEA103988349 WGS data

  The iPSC line UKKi022-C / SAMEA103988349 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 UKKi022-C is available for research use at www.EBiSC.org.

  Dataset EGAD50000001084

• WTSIi009-A / SAMEA2593858 WGS data

  The iPSC line WTSIi009-A / SAMEA2593858 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 WTSIi009-A is available for research use at www.EBiSC.org.

  Dataset EGAD50000001085

• EDi016-B / SAMEA4767418 WGS data

  The iPSC line EDi016-B / SAMEA4767418 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-B is available for research use at www.EBiSC.org.

  Dataset EGAD50000001086

• EDi017-C / SAMEA4771168 WGS data

  The iPSC line EDi017-C / SAMEA4771168 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 EDi017-C is available for research use at www.EBiSC.org.

  Dataset EGAD50000001087

• UOXFi008-B / SAMEA103887561 WGS data

  The iPSC line UOXFi008-B / SAMEA103887561 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 UOXFi008-B is available for research use at www.EBiSC.org.

  Dataset EGAD50000001089

• 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-A / SAMEA17624668 WGS data

  The iPSC line UKKi019-A / SAMEA17624668 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-A is available for research use at www.EBiSC.org.

  Dataset EGAD50000001094

• 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

• Bulk-RNAseq from human nerve fascicles and Schwann cells

  Bulk-RNAsequencing from human nerve fascicles from patients with polyneuropathies, and human Schwann cell cultures isolated from said nerve fascicles, in comparison to control human Schwann cell cultures and a referential fibroblast culture.

  Study EGAS50000000737

• CAYA glioma sequencing data

  Low pass WGS and targeted glioma panel sequencing of low and high-grade gliomas in children, adolescent, and young adult patients.. File type is paired-read fastq files (2 per sample). Sequencing was performed on Illumina NextSex instruments. Genes covered on panel: TP53, H3F3A, HIST1H3B, HIST1H3C, IDH1, IDH2, KRAS, PIK3CA, TERT promoter, PTPN11, FGFR1/2/3, MYB, BRAF, MYBL1, EGFR, PDGFRA, MYCN, MYC, CDKN2A.

  Dataset EGAD50000000560

• Saliva Microbiota of Finnish children from the PANIC study

  Saliva microbiota of 407 participants of PANIC study, is profiled with 16S rRNA gene sequencing (regions V3-V4). Amplification was performed using the TruSeq-switched tail amplicons. The sequencing was performed using the 2 × 301 base-pair on the Illumina MiSeq PE300 platform. Data includes information on sex, age, and caries status of participants. File format is fastq.gz.

  Dataset EGAD50000000989

• 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

• Total RNA sequencing of fibroblasts from an individual with fragile X syndrome

  Total RNA sequencing of fibroblasts from an individual with a methylated CGG repeat >200x in the FMR1 5'UTR. Libraries were prepared with total RNA with Ribo-Zero ribosomal RNA depletion (illumina), and sequenced paired-end, 75bp on a NextSeq 550 system. This dataset contains three RNA-sequencing replicates from the same cell line.

  Dataset EGAD50000000920

• Paired-end Whole Exome-seq analysis of the 3D evolution of glioma cell populations. Part 1.

  Dataset contains Exome sequencing data (aligned and base quality score recalibrated BAM files) for 236 tumor samples + matched normal from blood, collected from 21 patients with adult diffuse glioma. The majority of these samples were spatially-mapped during sample collection, enabling the genomic information derived from them to be mapped in 3D space.

  Dataset EGAD00001005221

• WGA_Fulani_Database

  In total, 329 DNA samples were genotyped on the Illumina Infinium H3Africa Consortium array (designed for 2,271,503 SNPs; using BeadChip type: H3Africa_2019_20037295_B1). Genotyping was performed at the SNP&SEQ Technology Platform (NGI/SciLifeLab Genomics, Sweden). WGA Fulani dataset includes individuals from the following populations: 33 BurkinaFaso_FulaniBanfora, 32 BurkinaFaso_FulaniTindangou, 33 Mali_FulaniDiafarabe, 35 Cameroon_FulaniTcheboua, 34 Chad_FulaniBongor, 24 Chad_FulaniLinia, 25 Niger_FulaniAbalak, 32 Niger_FulaniAder, 31 Niger_FulaniDiffa, 20 Niger_FulaniBalatungur, and 30 Niger_FulaniZinder.

  Dataset EGAD50000000654

• 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

• ChIP seq samples

  Dataset contains 12 ChIP-Seq samples sequenced on the Illumina NextSeq500 sequencer. 3 samples are control samples (HcAct-Chip 1,HcAct-Chip 2,HcAct-Imput 2) 9 samples are case samples (HcAct2DG-Chip 1,HcAct2DG-Chip 2,HcAct2DG-Imput 1,JIAAct-Chip1,JIAAct-Chip2,JIAAct-Imput2,JIAAct2DG-Chip1,JIAAct2DG-Chip2,JIAAct2DG-Imput2)

  Dataset EGAD50000001188

• RNA seq samples

  Dataset contains 12 RNA-Seq samples sequenced on the Illumina NextSeq500 sequencer. 6 samples are controls (D1-Tact-Plasma,D2-Tact-Plasma,D3-Tact-Plasma,D1-TUnstim-Plasma,D2-TUnstim-Plasma,D3-TUnstim-Plasma) 6 samples are case (D1-Tact-SF,D2-Tact-SF,D3-Tact-SF,D1-TUnstim-SF,D2-TUnstim-SF,D3-TUnstim-SF)

  Dataset EGAD50000001189

• Target sequencing for 53 synovial sarcoma patients

  This dataset contains 138 .bam files sequenced with Illumina NovaSeq 6000. The files with the variant calling performed to the sequencing data, as well as the clinical data (phenotype) extracted during the sample extraction.

  Study EGAS50000000522

• 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

• McQuillin_Global_WES_Schizophrenia

  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 1,623 Schizophrenia, Bipolar and 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 EGAD50000001316

• 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

• Synthetic - GDI synthetic dataset (Population 11 Finland, Subgroup 2)

  Synthetic - This dataset contains the pheno-clinical and genomic information of 42046 individuals from COVID Population 11 Finland, Subgroup 2. 2010 are affected by Phenotype 1, 2010 are affected by Phenotype 2, 188 are affected by Phenotype 1 and 2, and 37838 are control. The dataset also contains the information about the smoking habits of each individual.

  Dataset EGAD50000000955

• H3Africa AWIGEN Pilot MetaboChip

  Pilot study on the interplay between genetic, epigenetic, and environmental risk factors for obesity and related cardiometabolic diseases with 973 samples from South Africa genotyped on Illumina Human MetaboChip array.

  Dataset EGAD00010001258

• RNA-Seq profiles from the CheckMate-649 Clinical Trial

  This dataset contains RNA sequencing (RNAseq) data of 814 patients from the CheckMate 649 clinical trial whose ICF allows data deposition into a public repository. Gene expression profiling was performed retrospectively using RNAseq on a subset of baseline tumor samples. Paired-end FASTQ files were processed on Seven Bridges platform (Seven Bridges Genomics).

  Dataset EGAD50000001105

• scRNAseq and scTCRseq data from tumor-infiltrating lymphocytes

  SCRNAseq and TCRseq are performed using 10X genomics technology on lymphocytes from tumor of 8 individuals (4 different conditions and 2 replicates per condition): - ISO : isotype sample_1 - ISO_dup :isotype sample_2 aPD1 : sample anti-PD1_1 aPD1_dup :sample anti-PD1_2 aCTLA4: sample anti-CTLA4_1 aCTLA4_dup :sample anti-CTLA4_2 combo : sample_anti-PD1_anti-CTLA4_1 combo_dup : sample_anti-PD1_anti-CTLA4_2

  Dataset EGAD50000001214

• Multi-omics profiling identifies two epithelioid sarcoma molecular subtypes with distinct signaling and immune characteristics

  Bulk RNA Sequencing of 33 epithelioid sarcomas (EpS) and 3 extracranial extra-renal rhabdoid tumors (EERT) Whole-exome sequencing of 30 EpS and 3 EERT Single-cell RNA Sequencing of 8 EpS Visium Spatial Transcriptomics of 3 EpS

  Dataset EGAD50000001419

• Picuris Pueblo oral history and genomics reveal continuity in US Southwest

  Following the decision of Picuris Pueblo to study their population history using DNA, this project generated 16 ancient and 13 present-day genomes from the Pueblo, spanning 1,000 years of history.

  Study EGAS50000000855

• 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

• Whole-exome and RNA sequencing data from a uveal melanoma patient with multi-regional sampling

  This dataset includes whole-exome sequencing (WES) and RNA sequencing (RNA-seq) data from a uveal melanoma patient. Tumor samples were obtained from three distinct regions, each with matched RNA-seq and WES data. Additionally, WES data from the patient’s peripheral blood mononuclear cells (PBMCs) is provided as a germline reference.

  Dataset EGAD50000001422

• Targeted sequencing data of cfDNA, archival tissue, and WBC from 226 patients with mUC

  Targeted tissue (n=210), cfDNA (n=402), and WBC (n=245) Illumina sequencing of metastatic urothelial carcinoma patients. All cfDNA is collected in the metastatic setting, while archival tissue is from across the disease course. White blood cell (WBC) samples are used as patient matched germline samples. All files are in paired-end fastq format.

  Dataset EGAD50000001571

• M116 CHIP Amplicon Sequencing

  Genomic DNA was obtained from M116 peripheral blood sample and was used for targeted deep sequencing (TDS) studies. Barcoded libraries were prepared according to the manufacturer’s instructions, using a probe-based panel (KAPA HyperCap, Roche®) targeting frequently mutated regions of 50 myeloid-related genes. Samples were run on a MiSeq (Illumina®) sequencer for paired-end 2x75 bp reads with a mean coverage of 1000X.

  Dataset EGAD50000001287

• WES dataset for SJMPAL011911 with different treatments

  This dataset includes whole exome sequencing (WES) data from PDX samples post-drug treatment (N=1 vehicle, N=1 gilteritinib, N=1 venetoclax and N=1 VenGilt). Bam files are provided for each sample. The VenGilt-treated sample underwent whole genome amplification using the Qiagen REPLI-g kit (#150345) prior to sequencing due to the very low cell number.

  Dataset EGAD50000001425

• 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

• WGS data of paediatric TCF3::PBX1 acute lymphoblastic leukemia (set2)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of one TCF3::PBX1 ALL patient (ALLT-376). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (90x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000001795

• WGS data of pediatric TCF3::PBX1 acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of one TCF3::PBX1 ALL patient (ALLT-335). Sequencing library was made using standard PCR-based WGS library preparation (PCR+), using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (90x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000001796

• RNA-sequencing of platelets and immortalized megakaryocyte cell lines for inherited thrombocytopenia

  Total RNA-sequencing of platelets and immortalized megakaryocyte cell lines for inherited thrombocytopenia. Libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold kits. The samples were paired-end sequenced using the NovaSeq 6000 platform at a depth of 60 million reads per sample with a read length of 100 base pairs.

  Dataset EGAD50000001818

• 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

• APC-related multiple salivary gland lesions

  This study aims to investigate the genetic and molecular mechanisms underlying a novel phenotype of attenuated familial adenomatous polyposis (AFAP), where affected individuals develop multiple salivary gland tumours, including basal cell adenomas and adenocarcinomas.

  Study EGAS50000001159

• Spatial transcriptomics

  This dataset contains raw sequencing and processed data of spatially resolved transcriptomes. The data were generated with 10x Visium probe-based assay on FFPE tissues of 30 ST-EPN tumour resections. Raw data contain two-lane fastq files of the sequencing. Processed data contain aligned and filtered .h5 counts matrices as well as positional files as generated by 10x SpaceRanger.

  Dataset EGAD50000001876

• WGS

  A genome-wide approach based on next generation sequencing (NGS) is performed on trios ( Patient+ Father + Mother) with SAID in order to identify known and new gene variants associated with certain forms of the disease. WGSwas performed on frozen PBMCs. DNA was extracted using the QIAamp DNA Blood Midi Kit and quantified with Nanodrop. Sequencing was done on a NovaSeq 6000 with S4 flow cells, targeting 30× coverage.

  Dataset EGAD50000002024

• RNU2-2 splicing signature RNA-Seq

  This dataset is composed of RNA-Seq samples: 49 controls which are probands without snRNA rare variants and 19 affected probands with either monoallelic or biallelic variants in RNU2-2. RNA was extracted from short-term lymphocytes cultures. RNA-Seq libraries were obtained by hybrid capture of fragmented cDNA with RNA probes from exome v8 (Agilent)

  Dataset EGAD50000002045

• Plasma cfDNA dataset from healthy donors and cancer patients

  The dataset contains 424 paired-end raw fastq files of 224 plasma cfDNA samples from healthy donors and cancer (Ewing Sarcoma, CIC) patients. WGS and methylation binding domain sequencing was performed at 2 × 150 bp on an NovaSeq6000 or NextSeq 500. 200 samples underwent both WGS and methylation binding domain sequencing. 24 samples underwent only WGS.

  Dataset EGAD50000002051

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

  This study 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). The aim of the project is to detect genomic variants (rare and inherited variants) in regulatory regions that contribute to autism.

  Dataset EGAD50000002029

• MB_COMICS_Methylome

  Medulloblastoma (MB) is the most common malignant brain tumor in children. It is a neuroectodermal tumor located in the cerebellum. International consensus recognizes four distinct subgroups of MBs including Wingless (WNT), Sonic Hedgehog (SHH), Group 3 (G3), and Group 4 (G4) with distinct molecular characteristics, prognoses, and mortality rates in patients. Here, we have compiled and evaluated a large international MB cohort for which we generated methylome data for 369 primary MB patient samples.

  Dataset EGAD00010002669

• single cell RNA-seq data of 10 small cell lung cancer patients

  This dataset contains 10 paired fastq files sequenced on Illumina NextSeq 550 sequencer. Tumors were rapidly dissociated after the surgical procedure using the Miltenyi Biotec Human Tumor Dissociation kit (cat# 130-095-929). Libraries were constructed using the VDJ NextGEM v1.1 10x Genomics Chromium kit. Single cell RNA-seq analysis was performed using Seurat R package.

  Dataset EGAD50000002034

• Targeted sequencing data of cfDNA, archival tissue, and WBC from 208 patients with mUC

  Targeted tissue (n=81), cfDNA (n=319), and WBC (n=208) Illumina sequencing of metastatic urothelial carcinoma patients. All cfDNA is collected in the metastatic setting, while archival tissue is from across the disease course. White blood cell (WBC) samples are used as patient matched germline samples. All files are in paired-end fastq format.

  Dataset EGAD50000002089

• WGS data of paediatric BCR::ABL1 acute lymphoblastic leukemia

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of one BCR::ABL1 ALL patient (ALLT-399). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set Kit (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using NovaSeqX Plus.

  Dataset EGAD50000002185

• Batch-corrected 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.

  Dataset EGAD50000002169

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set5)

  The dataset includes FASTQ and BAM/CRAM files from diagnostic and matched remission (control) samples of two B-other ALL patients (ALLT-396, ALLK-131). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set. Both diagnostic (90x) and remission (30x) samples were sequenced using NovaSeqX Plus.

  Dataset EGAD50000002160

• CIAO Clinical Trial

  Whole exome and RNA sequencing for samples from CIAO (Checkpoint Inhibitors Assessment in Oropharynx cancer) (NCT03144778) clinical trial testing neoadjuvant anti-PD-L1 durvalumab with or without the anti-CTLA-4 tremelimumab in oropharynx cancer

  Study EGAS50000001174

• The dataset of Detection and characterization of lung cancer using cell-free DNA fragmentomes on NovaSeq 6000 at 1-2x coverage

  The dataset contains 364 CRAM files from whole-genome next-generation sequencing on the Illumina NovaSeq 6000 at 1- 2x coverage. These are plasma samples from healthy individuals and patients with cancer.

  Dataset EGAD50000001961

• Using Exome-sequencing to characterize the resistance to lirafugratinib

  We characterized 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 EGAS50000001371

• GATA1 scD&D-seq integrated with Multiome

  Ex vivo differentiation experiments were performed using human CD34+ hematopoietic stem and progenitor cells along the erythropoietic trajectory at multiple timepoints (differentiation days 0, 5, 8, 18, and 24). Simultaneous profiling of transcriptome, chromatin accessibility, and GATA1 binding were performed by integrating D&D-seq with 10X Multiome.

  Dataset EGAD50000002299

• TenK10K Phase 1: scRNA-seq AnnData objects

  Single cell RNA-sequencing data for PBMCs from the Tenk10k Phase 1 cohort (1925 individuals post-QC). Libraries were prepared using the 10x Genomics 3’ Chromium Next GEM Single Cell HT V3.1 kit and sequenced on the NovaSeq 6000 platform. Reads were mapped to the GRCh38 reference genome with Cellranger, and count matrices were preprocessed using Scanpy.

  Dataset EGAD50000002379

• Exome sequencing data for the DIRECT study.

  This dataset contains all available fastq files for gemline, baseline plasma/biopsy, and response assessment patient samples for the DIRECT study. The total number of samples was 729 (188 germline, 190 baseline plasma, 159 baseline biopsy, and 192 response assessment). The dataset files were generated from targeted (exome) Illumina sequencing performed on paired biopsy tissue and plasma cell free DNA.

  Dataset EGAD50000001409

• Diverse Cellular Composition in Alveolar Rhabdomyosarcoma Revealed by Single Cell RNA Sequencing

  Using single cell RNAseq data to characterize tumor composition and cellular states for Alveolar Rhabdomyosarcoma. We find that that ARMS tumors harbor phenotypically and transcriptionally distinct malignant subpopulations within an immune-influenced microenvironment.

  Study EGAS50000001564

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set2)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of two hyperdiploid ALL patients (ALLT-315, ALLT-320). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), using TruSeq DNA PCRfree library preparation kit v1. Both diagnostic (60x) and remission (30x) samples were sequenced using Illumina HiSeq X.

  Dataset EGAD50000002426

• Whole exome sequencing variant data for Mendelian disorders cohort

  This dataset contains whole exome sequencing variant data (VCF files) from individuals with suspected Mendelian disorders, including sickle cell disease, muscular dystrophy, haemophilia, and Fanconi anemia. Variant calling was performed using the Illumina DRAGEN pipeline, with downstream variant prioritisation conducted using the Zi-Mendelian bioinformatics pipeline. The dataset supports research into rare genetic diseases and genomic variation in African populations.

  Dataset EGAD50000002453

• Biomodal duet +modC sequencing of endometrial cancer plasma cfDNA samples

  This dataset contains biomodal sequencing data generated using the duet + modC assay from plasma-derived cell-free DNA of endometrial cancer patients and healthy donors. Sequencing was performed on an Illumina NovaSeq 6000. Dataset includes raw sequencing FASTQ files. Duet +modC output enables whole-genome profiling of both genetic variation and DNA methylation.

  Dataset EGAD50000002261

• TruSight Oncology 500 ctDNA targeted sequencing data from endometrial cancer patients

  This dataset contains targeted sequencing data generated using the TruSight Oncology 500 ctDNA v2 assay from plasma-derived cell-free DNA of dMMR endometrial cancer patients, at baseline and C3D1 of immunotherapy. Sequencing was performed on Illumina NovaSeq600. Dataset includes aligned sequencing files in BAM format generated using the DRAGEN TruSight Oncology 500 ctDNA v2.6.0 analysis pipeline.

  Dataset EGAD50000002262

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 17)

  The dataset contains whole genome sequencing data of 26 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 86 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.

  Dataset EGAD50000002409

• A_study_of_the_molecular_pathogenesis_of_Splenic_Marginal_Zone_and_Diffuse_Large_B_Cell_Lymphoma

  We will perform exome sequencing on selected cases of splenic marginal zone lymphoma (SMZL) and diffuse large B-cell lymphoma (DLBCL) in order to characterise their genetic makeup and identify biomarkers for prognosis and prediction of treatment response.

  Study EGAS00001000335

• TCELL_PILOT_ATAC_SEQ

  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 EGAS00001000758

• Molecular analysis of cancer genomes in children with Lynch syndrome: exploring causal associations

  Molecular characterization of 20 tumors of 18 children with Lynch syndrome to investigate causality. This characterization includes the investigation of second hits, tumor mutational load, mutational signatures and MMR protein expression.

  Study EGAS00001006992

• Lymphocyte_RNA_profiling

  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 EGAS00001000564

• Whole exome sequencing of papillary thyroid carcinoma in the Chinese population

  Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Here we submitted the sequencing results for PTC using 91 tumor-normal pairs through exome sequencing in the Chinese Han population.

  Study EGAS00001001268

• Single Cell RNAseq of blood and tumor from renal cancer patients

  Single-cell RNASeq (scRNAseq) showed that IL8 is primarily expressed in circulating and intratumoral myeloid cells and high IL8 expression was associated with the downregulation of the antigen presentation machinery in myeloid cells.

  Study EGAS00001004230

• Breast_Cancer_Matched_Pair_Cell_Line_Whole_Genomes

  We propose to definitively characterise the somatic genetics of matched pair breast cancer cell lines through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000166

• Y_chromosome_mis_segregation_in_the_DLD_1_cell_line

  Study of the well-established DLD-1 colorectal cancer cell line, engineered with an inactivatable Y centromere that leads to mis-segregation. The goal is to gain insights into the mechanism of chromothripsis due to chromosome mis-segration.

  Study EGAS00001002551

• Preclinical_evolution_of_haematological_malignancies_

  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 EGAS00001002128

• 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

• Whole genome sequencing and whole exome sequencing of mucosal melanoma

  We conducted whole genome sequencing of 5 mucosal melanomas and their matched DNA from blood. We conducted whole exome sequencing of a further 5 mucosal melanomas and their matched DNA from blood.

  Study EGAS00001000474

• CELM

  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 EGAS00001002261

• Presence of fungal infection in brains of patients with Parkinsons disease (PD)

  Isolation of fungi in infected neural tissues in patients with Parkinson's disease. Here we used next generation sequencing of Internal Transcribed Spacer (ITS) regions, by PCR amplicons (NGS ITS amplicon analysis).

  Study EGAS00001003644

• Characterization of Arabian Peninsula whole exomes

  We conducted whole exome sequencing (using the SureSelect Human All Exon V5 + UTRs target enrichment kit) of 90 individuals from AP (23 from Saudi Arabia, 24 from Yemen, 24 from Oman and 19 from UAE).

  Study EGAS00001006487

• Triple_Negative_Breast_Cancer_Whole_Genomes

  We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000092

• Transcriptome_Sequencing_of_Cancer_Cell_Lines

  In this study we will sequence the transcriptome of Verified Cancer Cell lines. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

  Study EGAS00001000261

• Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer

  Pancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Here we report analysis of gene mutation, copy number and RNA expression of 57 sporadic well-differentiated pNETs.

  Study EGAS00001003038

• Whole-exome analysis of corticotropin-independent Cushing's syndrome

  We performed WES for 8 cases with corticotropin-independent Cushing’s syndrome, in whom paired tumor and normal DNA was obtained from fresh frozen adenomas and either normal adrenal tissues or peripheral blood, respectively.

  Study EGAS00001000661

• Genetics_and_Networks_of_Congenital_Heart_Defects

  Exome sequencing of families with Congenital Heart Defects of diverse sub-phenotypes. Comprises both parent-offspring trios for sporadic cases and multiplex families. Collaboration with David Brook, University of Nottingham. Funded by the British Heart Foundation.

  Study EGAS00001000762

• Genome sequencing of oesophagus atresia families

  To gain insight into gene variants and genes associated with isolated Oesophageal atresia (OA) we conducted whole genome sequencing on samples from three families with recurrent cases affected by congenital and isolated tracheoesophageal fistula (TEF).

  Study EGAS00001004394

• Characterization_of_iPSC_derived_macrophages___cardiovascular_pilot

  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 EGAS00001000876