22941 results for "ega"

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• WGBS data for ependymomas and normal controls (fetal and adult)

  Whole genome bisulfite sequencing data for 6 ependymomas plus 3 fetal controls (f1, f2, f4) and 3 adult controls (a2, a3, a4). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142).

  Dataset EGAD00001000966

• Cancer-Normal chronic myeloid leukaemia sequencing data for "A comparative analysis of algorithms for somatic SNV detection in cancer", Bioinformatics 29 (2013) 2223

  This dataset contains the fastq sequencing data collected from bone marrow DNA of a chronic myeloid leukaemia patient at time of diagnosis.

  Dataset EGAD00001000967

• Whole Genome Sequencing of 18 sequential samples from 3 CLL patients

  Whole Genome Sequencing to track subclonal heterogeneity in 18 samples from 3 Chronic Lymphocytic Leukemia patients subjected to repeated cycles of therapy. NOTE: There are only 12 BAM files available to download. The other 6 files are missing.

  Dataset EGAD00001000972

• Transposome Bisulfite Sequencing

  DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform.

  Dataset EGAD00001001028

• APCDR Uganda GWAS - UG2G dataset: Whole genome low depth sequence data for 2000 Ugandans (BAMs).

  Low depth (4x) Illumina HiSeq raw sequence data for 2000 Ugandans from various ethno-linguistic group from rural South-West Uganda (related individuals included).

  Dataset EGAD00001001639

• Genomic alteration in Korean Young Age Diffuse Gastric Cancers

  To identify recurrent somatic alterations in this unique subset of gastric cancers, whole exome and SNP6 analyses were performed using frozen cancer tissue. The somatic mutation analyses were also performed using blood of the same patients.

  Dataset EGAD00001001984

• Data files for PCGP SJACT RNASEQ

  This dataset contains RNA-Seq files for the SJACT cohort associated with the paper "Genetic landscape of pediatric Adrenocortical Tumor". In this paper, we analyse 37 adrenocortical tumours (ACTs) by whole-genome, whole-exome and/or transcriptome sequencing.

  Dataset EGAD00001002680

• BLUEPRINT DNA methylation profiles of human hematopoietic progenitors

  DNA methylation was analyzed for stem/progenitor cell types and terminally differentiated cell types of the human blood lineage (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3, MK, CD4+ Tcell, CD8+ Tcell, Bcell, NK, Neut, Mono).

  Dataset EGAD00001002732

• Exome sequencing of 7-member healthy family (father, mother, their three biological daughters and monozygotic twin sons)

  The dataset contains exome sequencing data of seven healthy family members, all in FASTQ format. The samples were taken from peripheral blood mononuclear cells. Furthermore, corresponding proteomics data are available as well.

  Dataset EGAD00001004949

• Highly recurrent U1 snRNA mutations drive alternative splicing in SHH medulloblastoma

  Highly recurrent U1 snRNA mutations drive alternative splicing in HH medulloblastoma

  Dataset EGAD00001004958

• Skin Fibroblast Transcriptome of Type 2 Diabetic Patients

  Comparative analysis of transcriptomes of skin fibroblasts in 17 Type 2 Diabetic individuals by RNA sequencing.

  Dataset EGAD00001004980

• Expression data

  This dataset contains the RPKM and raw read counts of expression for all the individuals. This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity.

  Dataset EGAD00001005039

• Clinical phenotypes/covariates

  This dataset contains the clinical phenotypes/covariates information for all the individuals. This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity.

  Dataset EGAD00001005040

• Cancer and germline exomes, and cancer RNA-seq consisiting of FASTQ paired-end reads from melanoma and lung cancer samples

  Cancer and germline exomes, and cancer RNA-seq consisiting of FASTQ paired-end reads from melanoma and lung cancer samples

  Dataset EGAD00001005097

• EGAS00001003405 combined RNA, WES, WGS data of 16 gastrointestinal tumor patients

  50 samples of 16 individuals with Gastrointestinal Tumor. Patients were sequenced in various combinations of WGS, Exome and RNA sequencing.

  Dataset EGAD00001005113

• Targeted deep sequencing

  T200 caner panel sequencing on primary and metastatic sites from highly clinically annotated HGSC samples. Samples were obtained pre-treatment based on a laparoscopic triage algorithm from patients who underwent R0 tumor debulking, or received neoadjuvant chemotherapy (NACT) with excellent (ER) or poor response (PR).

  Dataset EGAD00001005239

• Benchmarking CRISPR Whole-genome Drop-out Screen - B&S (2019-08-07)

  This study is a benchmarking exercise to explore potential source of variation between different CRISPR drop out libraries. . This dataset contains all the data available for this study on 2019-08-07.

  Dataset EGAD00001005233

• GRAIL Metadata

  Metadata summarizes participants (n=198), samples (n=396), basic clinical information, and analysis. analysis1: raw sequencing reference alignment files (bam/bai) analysis2: error-corrected sequencing reference alignment files (bam/bai) analysis3: variant calling using error-corrected sequencing reference alignment (vcf)

  Dataset EGAD00001005302

• SF11979 snATAC seq IDHR132H Wildtype GBM Female

  SF11979 snATAC, IDHR132H WT GBM Female, 76 Single Nuclei ATAC seq data from high grade human glioma samples. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005418

• SF11979 snRNA-Seq Primary GBM IDHR132H Wildtype Female

  Single Nuclei Primary GBM IDHR132H Wildtype. Female 76. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005430

• HEMa_LP

  This dataset contain WGBS sequencing result of HEMa_LP. The cells were cultured in Medium 254 supplemented with PMA-Free Human Melanocyte Growth Supplement-2 (HMGS-2) under 37°C,5% CO2.

  Dataset EGAD00001005486

• Familial adult myoclonic epilepsy type 1 in Sri Lankan and Indian families

  Whole genome sequencing data from four affected and one unaffected individuals from two families with familial adult myoclonic epilepsy, one of Sri Lankan origin and one of Indian origin. BAM files aligned to hg19 reference genome.

  Dataset EGAD00001005777

• Multi-region sequencing of a RET fusion positive cancer patient

  Deep WGS sequencing (160x) of 2 different sites of disease of a patient with a RET fusion positive cancer. Amplicon sequencing of 19 other sites of the same patients for the RET fusion.

  Dataset EGAD00001005776

• Analysis File for 87 Argentinean individuals

  VCF for 87 Argentinean samples. Only SNPs (no indels) that passed the Affymetrix QC. Data from Luisi et al. 2020. Plos One. Fine-Scale Genomic Analyses Of Admixed Individuals Reveal Unrecognized Genetic Ancestry Components In Argentina. Reference Allele column does NOT contain reference allele from genome assembly.

  Dataset EGAD00001006227

• The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia

  RNA-seq data for ALL patients as described in "The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001006335

• Medulloblastoma whole and focused exome sequencing (n=13 patients, n=37 samples)

  Whole exome sequencing: 24 samples matched tumor-normal and one matched CSF. Focused exome sequencing: 17 samples matched tumor-normal-2 time point CSF.

  Dataset EGAD00001006387

• RNA-Seq data of VDH15 cells with and without deletion of NSUN3

  paired RNA-Seq data of VDH15 cells with and without deletion of NSUN3. The 11 samples were sequenced on HiSeq 4000 and prepared with SmarTer low input RNA and Chip NEBNext kit.

  Dataset EGAD00001006560

• COVID-19 Postmortem Lung snRNA-seq

  A deeper understanding of the pathological mechanisms of SARS-CoV-2 infection is required to combat COVID-19. Through this dataset, we analyze postmortem lung cells from patients that are infected/uninfected with SARS-CoV-2 with snRNA-seq.

  Dataset EGAD00001006584

• RNASeq files for Mullighan TXVI dataset

  RNASeq files for paper titled "Prognostic and therapeutic significance of leukemia subtypes and minimal residual disease measurements in pediatric acute lymphoblastic leukemia treated with contemporary risk-directed trial: a cohort study"

  Dataset EGAD00001006609

• WES FASTqs

  Whole exome sequencing FASTq files from 469 pre-treatment tumors from IMvigor210, POPLAR and IMmotion150, with matched PBMC samples.

  Dataset EGAD00001006632

• 1000IBD.eQTL.study.release.eQTLsummary&GeneTable

  eQTLsummary&GeneTable from eQTL study in 299 intestinal biopsy samples from IBD

  Dataset EGAD00001006789

• HV31 - PacBio long-read circular consensus (CCS) senquencing

  PacBio long-read circular consensus (CCS) sequencing data for individual HV31 generated on PacBio Sequel II instrument, using size-selected (10-15 kb) DNA from CD14+ monocytes, to a sequencing depth of ~12×. Sequencing was performed at the Wellcome Sanger Institute.

  Dataset EGAD00001006979

• Exome sequencing data for 40 cases of alopecia areata and vitiligo

  Sequencing of independent unrelated cases of alopecia areata (total/ universal) and vitiligo (>10%, affected family member). DNA obtained from blood

  Study EGAS00001003831

• 16S rRNA Rectal Mucus

  16S rRNA sequencing of rectal mucus samples from patients suspected to have colorectal cancer. This is 1 of 4 sequencing experiments on the same sample type.

  Study EGAS50000001262

• How to encrypt files with EGACryptor

  File preparation Due to the processes used at the EGA for file archival the use of non-alphanumeric characters in a filename will cause issues in archival. By convention whitespaces in filenames are to be avoided and should be replaced with the underscore character (_). Before encrypting your files please make sure that any files that will be uploaded to EGA do not use special characters such as # ? ( ) [ ] / \ = + < > : ; " ' , * ^ | &  Crypt4gh EGACryptor Files encrypted with EGACryptor must be uploaded via FTP EGACryptor The EGACryptor v.2.0.0 is a JAVA-based application which enables submitters to produce EGA compliant encrypted files along with files for the encrypted and unencrypted md5sum for each file to be submitted. The application will generate an output folder that will by default mirror the directory structure containing the original files. This output folder can subsequently be uploaded to the EGA FTP staging area via an FTP or Aspera client. Download EgaCryptor Download EgaCryptor Using the EgaCryptor Using the EgaCryptor Encrypting single file Encrypting multiple files Encrypting all files in folder Points to note Troubleshooting Troubleshooting Download EGACryptor The required jar files can be obtained by downloading EgaCrytptor jar file After the file has been downloaded, extraction of the zipped archive is required. The EGACryptor has been built to work with Java Runtime Environments from version 6 and above and with the OpenJDK Environment. Please refer to the relevant resources for installation guidance. Installing the latest version of the OpenJDK will include the JCE files. If your installation of Java JRE is less than 1.8.0_151 will require the manual installation of the JCE Policy Files. You can verify the version of the Java SE Runtime Environment (JRE) installed by using the command: $ java -version If you need to install the JCE please follow the instructions below: Installing the JCE policy files (due to licensing terms and conditions the required policy files must be downloaded direct from the ORACLE website) : Download the unlimited strength JCE policy files (JRE 6 / JRE 7/ JRE 8) Uncompress and extract the downloaded file. This will create a subdirectory called JCE. This directory contains the following files: README.txt, COPYRIGHT.html, local_policy.jar and US_export_policy.jar Install the two policy JAR files by replacing the existing ones in your java home directory. Install the two policy JAR files by replacing the existing ones in your directory. The standard place for JCE jurisdiction policy JAR files is: /lib/security [Unix] or \lib\security [Win32] Notes: refers to the directory where the Java SE Runtime Environment (JRE) was installed. Additional performance enhancements that have been included in the EGACryptor V2.0.0: The ability to parallelise the processing of datasets through the use of the resources on a system. Multicore systems will allow the user to specify n-1 cores for an n-core system. The use of this feature on clusters may speed up the processing of datasets that have large file numbers but consult your local cluster guide to ensure that there are not monopolising resources that are needed by other system users. The default for this process remains single threaded. 3 levels of system usage can be specified. Full usage within the limits detailed above. A limited mode that will ensure that 50% of the system resources are available for other tasks. Maximum mode is limited to 75% of system resources, this allows encryption to be prioritised but allows for the system to be usable for light alternate tasks. Finally there is a throttling mode that allows you to specify the exact number of computational threads to be used. the EGACryptor is able to ingest a structured directory and will output a directory with the same structure containing the encrypted files along with the md5checksums for the plain and encrypted files. The entire output directory can then be uploaded to the EGA for archival. as with the input path, it is now possible to specify the output path. the options have been updated inline with the upgraded functionality. The tool can only be used via the command line. The EGACryptor is designed to perform a single task, encrypting your data, for upload of these files please refer to our uploading guide Using the EgaCryptor Below are the three ways on how the EGACryptor tool can be used: Encrypting a single file : java -jar ../EGA-Cryptor_2_0_0.jar -i example1.bam Encrypting multiple files : java -jar ../EGA-Cryptor_2_0_0.jar -i "example1.bam,example2.bam" Encrypting all the files within a folder java -jar ../EGA-Cryptor_2_0_0.jar -i path/to/target/directory By default the EGACryptor v2 will create a new output directory containing all encrypted files and the relevant checksums within the target directory. If a specific directory is desired this can be specified by using the -o flag. This can be achieved in a similar manner to the following example: java -jar ../EGA-Cryptor_2_0_0.jar -i /path/to/target/directory -o /path/to/output/directory The tool will output three files per input file: file.gpg ( encrypted file ) file.md5( file md5 sum value file ) file.gpg.md5 ( encrypted file md5 sum value file ) All output files must then be uploaded to your submission account using Aspera or FTP. Further documentation on how to upload files: FTP and Aspera. Points to note Remember to provide the path to EgaCryptor.jar and run the command from within the directory the file/s are located. ECryptor writes files to the source directory of your local file system, as a result you must have write-access permissions for the source directory. Troubleshooting If in doubt about the function of the EGACryptor it is recommended to first consult the built-in documentation. This can be accessessed by using the -h flag as stated in the following table. Built-in Commands Table: list of the command line options built into EGA-Cryptor v2.0.0. Command line Option Action --------------------- ----------- -f Set this option to allow application to create maximum threads to utilise full capacity of cores/processors available on machine -h Use this option to view the bult-in help menu * -i File(s) to encrypt. Provide file/folder path or comma separated file path if multiple files in double quotes -l Set this option to allow application to create maximum threads equals to 50% capacity of cores/processors available on machine -m Set this option to allow application to create maximum threads equals to 75% capacity of cores/processors available on machine -o Path of the output file. This is optional. If not provided then output files will be generated in the same path as that of source file (default: output- files) -t Set this option if user wants to control application to create maximum threads as specified. Application will calculate no. of cores/processors available on machine & will create threads accordingly Encryption Errors UnixFileSystem.createFileExclusively (Native Method) The error is thrown by UNIX ("UnixFileSystem.createFileExclusively(Native Method)"). It appears that the user does not have write-access to the file system where the file to be uploaded is located. EGACryptor always writes MD5 checksums into files before uploading them to the server, and these files are created in the same location where the uploaded file itself resides.Solution: address your directory permission issue and re-run the command. Install JCE Unlimited Strength Jurisdiction Policy files The JCE policy unlimited strength jurisdiction files should be installed according to your current java version If you are still facing difficulty with the EGACryptor v.2 after having consulted the documentation please contact the EGA Helpdesk.

  Documentation submission/data/file-preparation/egacryptor

• WTCCC case-control study for Hypertension

  WTCCC genome-wide case-control association study for Hypertension (HT) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000009

• EGAD00000000002

  WTCCC1 project samples from UK National Blood Service

  Dataset EGAD00000000002

• Genomics of Colorectal Cancer Metastases - Massively Parallel Sequencing of Matched Primary and Metastatic tumours to Identify a Metastatic Signature of Somatic Mutations (MOSAIC)

  Genomics of Colorectal Cancer Metastases - Massively Parallel Sequencing of Matched Primary and Metastatic tumours to Identify a Metastatic Signature of Somatic Mutations (MOSAIC)

  Dataset EGAD00001000080

• LITS

  Difference in gene expression values between case and control, log2 values. Blood transcriptome from women participating in the Norwegian Women and Cancer study (NOWAC) Post-genome Cohort taken up to eight years before brest cancer diagnosis. Illumina HumanWG-6 version 3 or Illumina HumanHT-12 expression bead chip, combined on identical nucleotide universal identifiers.

  Dataset EGAD00010001400

• Mutational consequences of precancerous liver disease

  Clonally expanded liver adult stem cell clones of healthy liver and cirrhotic liver (due to alcohol abuse, NASH and PSC), as well as biopsies of liver cancers were subjected to whole genome sequencing to determine the mutational impact of precancerous liver disease

  Dataset EGAD00001004105

• RFMix

  This dataset contains the per-chromosome RFMix input and output files for the local ancestry inference of 59 Aboriginal Australian genomes as reported in Malaspinas et al., 2016. Local ancestry was inferred assuming four mixing ancestral populations represented by: Europeans (27 individuals), Asians (29 individuals), Papuans (13 individuals) and Native Australians (7 individuals from the WCD region).

  Dataset EGAD00010001575

• usgwas-QC_imputed_update

  Understanding Society GWAS, samples that passed quality control, imputed to UK10K + 1000 Genomes combined reference panel

  Dataset EGAD00010000918

• A novel orthotopic patient-derived xenograft model of radiation-induced glioma following medulloblastoma

  DNA methylation arrays were performed to molecularly subtype these samples based on Capper D, Jones DTW, Sill M, et al. DNA methylation-based classification of central nervous system tumours. Nature. 2018;555(7697):469-474. doi:10.1038/nature26000

  Dataset EGAD00010002017

• Hepatitis B virus integrations promote local and distant oncogenic driver alterations in hepatocarcinogenesis

  This study contain the WGS and WEX aligned bam files and RNA-seq fastq files for human liver tumors.

  Dataset EGAD00001006426

• Colon cancer amplicon targeted sequencing study contaning WBCs, primary tumor tissue and plasma samples

  This dataset consists of amplicon targeted NGS paired-end raw data (FASTQ R1 and R2) obtained from 148 colon cancer patients. Specifically, we have 148 primary tumor tissue samples, 148 white blood cell samples, and 118 plasma samples collected at baseline.

  Dataset EGAD50000000084

• SARS-CoV2 mRNA-vaccination-induced Immunological Memory in Human Non-Lymphoid and Lymphoid Tissues

  This dataset includes combined single-cell RNA-Seq and T cell receptor profiling data for SARS-CoV-2 spike protein-reactive CD4+ T cells and NK cells from blood, liver, lungs, and bone marrow of human donors.

  Dataset EGAD50000000062

• Age-dependent association of clonal hematopoiesis with COVID-19 mortality in patients over 60 years

  Targeted sequencing with the Myeloid Solutions™ Panel (MYS) of SOPHiA Genetics for COVID-19 patientds (n=241 deceased, n=239 survivors).

  Dataset EGAD50000000001

• HGSC lines: ATACseq and RNAseq, pre- vs post-treatment with HKMTi-1-005

  Formation of a DAC to support the deposition of RNAseq and ATACseq data, from pre- vs post-treatment high-grade serous ovarian carcinoma cell lines. The lines include PEO1, PEO4, PEA2, OVCAR5, OVCAR8, and the treatment includes use of a novel epigenetic drug called HKMTi-1-005.

  Dac EGAC50000000034

• Dac for "MediMer: A versatile do-it-yourself peptide-receptive MHC class I multimer platform for tumor neoantigen-specific T cell detection"

  Dac for the Study "MediMer: A versatile do-it-yourself peptide-receptive MHC class I multimer platform for tumor neoantigen-specific T cell detection" registered for Frank Momburg, f.momburg@dkfz-heidelberg.de Marten Meyer, marten.meyer@dkfz-heidelberg.de

  Dac EGAC50000000064

• IBS-D RNA-seq raw data

  The data set consists of fastq raw files from RNA-seq of seven mucosal biopsies of the colon from seven patients, among them three patients with irritable bowel syndrome with diarrhea-predominant symptoms. Paired end sequencing on Illumina NovaSeq 6000 was used.

  Dataset EGAD50000000063

• Progressive multifocal leukoencephalopathy (PML)

  We generated RNAseq, ATACseq, Multiomics and CITEseq for patients with Progressive multifocal leukoencephalopathy (PML) to profile the chromatin accessibility, transcriptional profiles and surface proteins at single-cell level.

  Study EGAS50000000139

• PML complete dataset

  We generated single-cell transcriptomics, single-nuclei chromatin accessibility, CITE-seq and Multiomics of patients with PML. Pools are genetically multiplexed across donors, genotypic variation is included in this dataset to enable demultiplexing.

  Dataset EGAD50000000197

• Genomic analyses (WES, RNAseq, scRNAseq and scTCRseq) of triple negative breast cancer evolution

  This study explores the evolution of tumor and blood immune microenvironment and related mechanisms that shape breast cancer progression.

  Dataset EGAD50000000117

• Human TRIM24-MET fusion HGG RNA-seq

  Human RNA-seq data for TRIM24-MET fusion tumor primary samples and patient/PDOX-derived cell lines. Cells were treated with 0.1% DMSO or EC90 of MET inhibitors (capmatinib, cabozantinib, crizotinib) for 4 hours. BAM files containing aligned (and unaligned) reads to hg19 are provided.

  Dataset EGAD50000000194

• Netherlands Cancer Institute (NKI-AVL) general DAC

  Data is available under reasonable request. All data requests will be reviewed by the NKI IRB and must be supported by the Principal Investigator of the study. The researcher will need to sign a data access agreement with the NKI after approval. Go to https://ega.nki.nl to fill out the form to request access.

  Dac EGAC50000000055

• Oxidative DNA damage and ubiquitin proteasome system dysfunction underpins neurodegeneration in young adults with a DNA repair disorder

  Deposited here are WGS data generated from differentiated neural stem cells (NSCs) of NXPG-32 patient (XPG patient with neurodegeneration) and a matched healthy control CTRL-33.

  Dataset EGAD50000000232

• Oxidative DNA damage and ubiquitin proteasome system dysfunction underpins neurodegeneration in young adults with a DNA repair disorder

  Deposited here are time series bulk RNA-seq data generated from XP patients and controls as well as rescued patient hiPSC cells during cortical neuronal differentiation.

  Dataset EGAD50000000230

• Oxidative DNA damage and ubiquitin proteasome system dysfunction underpins neurodegeneration in young adults with a DNA repair disorder

  Deposited here are time series bulk RNA-seq data generated from isogenic wild-type (WT), XPA and XPG gene knockouts hiPSC cells during cortical neuronal differentiation.

  Dataset EGAD50000000228

• Clonally heritable gene expression imparts a layer of diversity within cell types

  Human datasets associated with paper 'Clonally heritable gene expression imparts a layer of diversity within cell types' published in Cell Systems

  Dataset EGAD50000000231

• The life-saving benefit of dexamethasone in severe COVID-19 is linked to a reversal of monocyte dysregulation

  Assessment of dexamethasone response in human lung through scRNA-seq analysis of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19.

  Study EGAS50000000203

• scRNA-seq of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 to assess dexamethasone response in the lungs

  Single-cell RNA-sequencing of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 with or without Dexamethasone treatment and for responders and non-responders was performed using 10x Genomics technology.

  Dataset EGAD50000000292

• Longitudinal WES data from MEMORI trial

  70 bam files generated from deep whole exome sequencing from samples from oesophageal adenocarcinoma from 17 patients. 17 bam files generated from deep whole exome sequencing from matching blood (germline control) from patients with oesophageal adenocarcinoma. Samples were collected within the clinical MEMORI trial.

  Dataset EGAD50000000355

• Cord blood progenitor CITE-seq dataset

  Sequencing results of single-cell transcriptome and antibody libraries from two biological experiments of cord blood progenitor cells. Four samples from different time points were processed using 10X Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Gene expression and antibody-derived libraries were sequenced separately.

  Dataset EGAD50000000405

• RNAseq of preneoplasia lung adenocarcinoma

  RNA sequencing of 168 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=38), adenocarcinoma in situ (AIS, N=22), minimally invasive adenocarcinoma (MIA, N=19) and invasive lung adenocarcinoma (ADC, N=38) and adjacent lung tissues (Normal, N=62).

  Dataset EGAD50000000395

• Whole genome sequencing of preneoplasia lung adenocarcinoma

  Whole genome sequencing of 42 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=5), adenocarcinoma in situ (AIS, N=7), minimally invasive adenocarcinoma (MIA, N=6) and invasive lung adenocarcinoma (ADC, N=8) and adjacent lung tissues (Normal, N=16).

  Dataset EGAD50000000396

• Single-cell BCR sequencing data of patients with T follicular helper cell lymphomas

  This dataset contains single-cell BCR sequencing data generated by the Cellranger pipeline (v3.1.0, 10X Genomics) from 5 LN and 1 PB samples of 5 patients with T follicular helper cell lymphomas (TFHLs) as well as 7 homeostatic LN (HLN) samples.

  Dataset EGAD50000000400

• Whole-exome sequencing data of patients with T follicular helper cell lymphomas

  This dataset contains WES data analyzed using the Genomon2 pipeline (v.2.6.2, https://github.com/Genomon-Project) from 14 patients with T follicular helper cell lymphomas (TFHLs). A list of somatic mutations called by the Genomon2 pipeline for each sample is provided as a txt file.

  Dataset EGAD50000000401

• Single-cell RNA sequencing data of patients with T follicular helper cell lymphomas

  This dataset contains single-cell count data generated by the Cellranger pipeline (v3.1.0, 10X Genomics) from 9 LN and 16 PB samples of 14 patients with T follicular helper cell lymphomas (TFHLs) as well as 7 homeostatic LN (HLN) samples.

  Dataset EGAD50000000402

• Single-cell TCR sequencing data of patients with T follicular helper cell lymphomas

  This dataset contains single-cell TCR sequencing data generated by the Cellranger pipeline (v3.1.0, 10X Genomics) from 9 LN and 16 PB samples of 14 patients with T follicular helper cell lymphomas (TFHLs) as well as 7 homeostatic LN (HLN) samples.

  Dataset EGAD50000000403

• INVADE cohort

  Cohort of bulk RNAseq data from DCIS, invasive and microinvasive breast cancer at diagnosis. This dataset covers 18 DCIS cases, 17 microinvasive and 20 primary invasive breast cancer.

  Study EGAS50000000219

• Exome sequencing analysis of BCP-LBL patients samples

  In order to perform comprehensive SNV and CNA analyses of a cohort of BCP-LBL patients, we performed whole exome sequencing of 41 tissue samples from BCP-LBL patients. Because the material was available as FFPE, the target coverage of the samples was >200x.

  Dataset EGAD50000000418

• Immuno-nephrology Data Access Committee Amsterdam UMC

  In this experiment we investigated kidney immunology in two autoimmune kidney diseases (ANCA-associated glomerulonephritis and Lupus Nephritis). Single cell transcriptome analysis of CD45+ immune cells from freshly retrieved kidney biopsies of 5 AGN patiënts, 1 disease-control with lupus nephritis (class II), and 1 "healthy" nephrectomy control was performed using 10X Genomics technology.

  Dac EGAC50000000024

• EBNA2 ChIP-Re-ChIP in primary B-cells infected with EBV virus

  EBNA2 ChIP-Re-ChIP in primary bulk B cells 4 days post EBV-infection with B95-8. DNA binding elements of the viral master regulator EBNA2, EBNA2-CBF transcription factor complex or EBNA2-EBF1 transcription factor complex were analyzed to identify virally targeted genes.

  Dataset EGAD50000000301

• WES and RNA-Seq of HCC biopsies and HCC derived Organoids

  We aimed to identify somatic mutations and transcriptional differences that could explain the resistance to Doxorubicin. This dataset includes RNA-Seq of HCC biopsies and Organoids and WES of Organoids.

  Dataset EGAD50000000060

• TCRseq

  T cell receptor sequencing of tumor samples. Briefly, DNAse I treated tumor RNA samples were subjected to library preparation using AmpliSeq Immune Repertoire Panel (Illumina) and sequenced using NextSeq500.

  Study EGAS50000000258

• Clones derived from early passage tumoroids of colorectal cancer

  We obtained different clones from early passage CRC tumoroids to study mutational signatures specific for truncal or private somatic alterations. These whole genome sequences are part of a larger study on the heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer.

  Dataset EGAD50000000152

• DCLRE1B/Apollo germline mutations associated with renal cell carcinoma impair telomere protection.

  We identified 2 germline mutations in the DCLRE1B gene encoding the Apollo protein by Whole Exome Sequencing (WES) in two families with inherited clear-cell Renal Cell Carcinoma. The raw data submitted here corresponds to WES performed on Genomic Platform at Gustave Roussy Institute.

  Dataset EGAD50000000311

• IMSGC and MultipleMS project MS patients from Spain

  Genotype and phenotype data on 151 MS patients from Spain. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002492

• IMSGC and MultipleMS project MS patients from Greece

  Genotype and phenotype data on 140 MS patients from Greece. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002493

• IMSGC and MultipleMS project MS patients from Norway

  Genotype and phenotype data on 575 MS patients from Netherlands. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002485

• IMSGC and MultipleMS project MS patients from Austria

  Genotype and phenotype data on 246 MS patients from Austria. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002487

• IMSGC and MultipleMS project MS patients from Netherlands

  Genotype and phenotype data on 209 MS patients from Netherlands. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002488

• IMSGC and MultipleMS project MS patients from UK

  Genotype and phenotype data on 943 MS patients from UK. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002491

• Genome-wide array data from Eivissan and Menorcan Individuals

  VCF file with autosomal genotypes from 22 and 20 Eivissan and Menorcan samples. Affymetrix Human Origins array was used to genotype the samples and the variants were lifted over to the hg38 human genome reference.

  Dataset EGAD50000000614

• cfRRBS data plasma healthy donors

  This is cfRRBS data produced from the cfDNA in plasma isolated from healthy, adult donors. Used as a reference for background signal in diseased (onclolytic) plasma cfDNA.

  Study EGAS50000000376

• WES analysis of tumor samples

  Whole exome sequencing was performed on paired tumor (N=8) from ER+ advanced breast cancer, obtained prior to combined CDK4/6i and endocrine therapy and at disease progression.

  Study EGAS50000000430

• DAC for "Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis"

  DAC for the data of "Cancer-associated fibroblasts promote drug resistance in ALK-driven lung adenocarcinoma cells by upregulating lipid biosynthesis" with: • Holger Sültmann • h.sueltmann@dkfz.de • German Cancer Research Center (DKFZ) • Ann-Kathrin Daum • a.daum@dkfz.de • German Cancer Research Center (DKFZ)

  Dac EGAC50000000076

• Whole Exome Sequencing of Bipolar cases and matched a cohort from Edinburgh, Scotland, UK

  Whole Exome Sequencing of 1260 Bipolar cases and matched controls performed at the Broad Institute on a cohort from Edinburgh, Scotland, UK. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing cram files

  Dataset EGAD50000000623

• Whole Exome Sequencing of Multiple Myeloma Patients

  We used whole exome sequencing (WES) data from 35 MM patients to evaluate possible mutational signatures and driver mutations associated with the patient’s clinical and cytogenetic characteristics.

  Study EGAS50000000394

• Transcriptional Reference Map of Human Natural Killler Cells

  Here we performed single-cell RNA sequencing of both bulk NK and sorted NK subsets to establish a transcriptional reference map of human natural killer cells.

  Study EGAS50000000014

• DELFI low-coverage WGS of plasma cfDNA

  The dataset "DELFI low-coverage WGS of plasma cfDNA" includes paired FASTQ files produced by WGS of 689 plasma cfDNA samples from 153 patients with colorectal cancer. WGS (100bp PE) was performed on a NovaSeq 6000 with a target depth of coverage of 8x.

  Dataset EGAD50000000630

• Inherited defects of piRNA biogenesis cause transposon de-repression, impaired spermatogenesis, and human male infertility

  Effect of biallelic variants in genes of the piRNA pathway on biogenesis of pachytene piRNAs. RNA isolated from snap frozen testicular tissue

  Study EGAS50000000397

• Exome - Uveal Melanomas

  Whole exome sequencing on 11 uveal melanoma samples and corresponding germline samples. Libraries were prepared using the SureSelectXT2 Clinical Research Exome V2 kit (Agilent, 5190-9500 and G9621B). Paired-end libraries (2 x 100 bp) were sequenced on HiSeq 2000/2500 or NovaSeq 6000 instruments (Illumina).

  Dataset EGAD50000000767

• Target sequencing of 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.

  Dataset EGAD50000000743

• CITE-seq data of six CK-AML patient samples

  We performed cellular indexing of transcriptomes and epitopes (CITE-seq) of six primary leukemia samples from CK-AML patients. The dataset contains BAM files for each individual sample (D1922 and R0836) or for the hashed pool (HIAML47-HIAML85, P9D-P9R)

  Dataset EGAD50000000633

• Strand-seq data of six CK-AML patient samples and three matching PDXs

  We performed strand-specific single-cell sequencing of six primary leukemia samples from four CK-AML patients. We also performed strand-specific single-cell sequencing of three matching patient-derived xenografts (PDXs). The dataset contains BAM files for each cell.

  Dataset EGAD50000000634

• BELLINI clinical trial bulk WES data: cohorts A & B

  WES data of 30 breast cancer primary tumors obtained from 30 unique patients from BELLINI clinical trial (cohorts A & B) and 30 matched blood samples. The data includes pretreatment samples. The included raw WES sequencing data in fastq format was generated using Illumina NovaSeq 6000.

  Dataset EGAD50000000809

• Spatial transcriptomics of hepatoblastoma

  10X Genomics Visium Spatial transcriptomics analysis of hepatoblastoma and adjacent normal liver. Spatial data of normal liver and PT2 (fastq files), and and PT13, PT14 and PT16 (bam files) using the Visium Spatial Gene Expression Solution. All samples, except PT13, were collected post-chemotherapy.

  Dataset EGAD50000000797

• Tumor Profiler Project - AML scRNA data

  The dataset contains single-cell RNA seq data from 23 patients with Acute Myeloid Leukemia (AML). Samples were collected from bone marrow or blood. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000000823

• Exome Sequencing of Multiple Localised Spiradenoma and Spiradenocarcinoma

  Tumor samples were microdissected from formalin-fixed, paraffin-embedded tissue and genomic DNA was extracted. DNA libraries were generated using xGen ssDNA & Low-Input DNA Library Preparation Kit (IDT). The libraries were enriched for the exome using xGen Exome Hyb Panel (IDT) and sequenced on DNBSEQ G400RS.

  Dataset EGAD50000000788