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• RNA-sequencing of a representative cohort of 209 AML cases

  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 EGAD00001007581

• Bone marrow microenvironment of 6 newly diagnosed myeloma patients using 10X Genomics scRNA- and TCR-sequencing

  10X Genomics scRNA- and TCR-sequencing (Chromium Next GEM Single Cell 5’ Reagent Kit v1.1) was performed on the plasma cell depleted mononuclear fraction of bone marrow aspirates from 6 patients with newly diagnosed multiple myeloma. Generated gene expression libraries were paired-end sequenced on the NovaSeq 6000 S2. Generated V(D)J libraries were paired-end sequenced on the NextSeq 550.

  Dataset EGAD00001009270

• SPECIAL: scRNA-seq

  Tumour biopsies were collected from twenty-three patients (46 samples) (of which 20 were matched) with locally advanced or metastatic melanoma (stage IIIB – stage IV). Library construction was done either with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (n = 16; 10x genomics, Cat#1000092) or the Chromium Single Cell A Chip Kit and 5’ Library & Gel Bead Kit (10x genomics, Cat#1000014). All libraries were sequenced on Illumina NextSeq, HiSeq4000 or NovaSeq6000 until sufficient saturation was reached (60% on average). The reference genome used in this study was GRCh38.

  Dataset EGAD00001009291

• Transcriptomic analyses of a large cohort of adult B cell acute lyphoblastic leukemia

  Total mononuclear cells (MNC) were isolated from peripheral blood (PB) or bone marrow (BM) samples of 105 Ph-/-/- (B-cell acute lymphoblastic leukemia [B-ALL] triple negative) and 31 Ph+ B-ALL adult patients using Lymphosep (Biowest, Nuaillé, France). A total of 15 samples from healthy subjects were processed including hematopoietic stem-progenitor cells (CD34+) from bone marrow specimens (n = 3), and bone marrow mononuclear cell samples (n = 3) from STEMCELL Technologies (Vancouver, Canada). PB MNC samples (n=5) and cord blood samples (n = 4). CD34+ cells were enriched from cord blood samples by immunomagnetic separation (CD34 MicroBead Kit, Miltenyi Biotec, Bergisch Gladbach, Germany).Libraries were prepared using the TruSight RNA Pan-Cancer Panel Kit (Illumina, San Diego, California, USA), following the manufacturer’s protocol. Sequencing was performed using the Illumina MiSeq instrument.

  Dataset EGAD00001010837

• DAC - The Netherlands Cancer Institute - Antoni van Leeuwenhoek

  Dac EGAC00001003316

• THE NOWAC BLOOD-BREAST CANCER COMMITEE DATA ACCESS AGREEMENT

  Dac EGAC00001000743

• The admixture histories of Cabo Verde

  Dac EGAC00001002727

• UK Biobank Access - http://www.ukbiobank.ac.uk/using-the-resource/

  Dac EGAC00001000641

• Cell types of the human retina and its organoids DAC

  Dac EGAC00001001703

• TNBC (COH_TNBC_RNAseq) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002518

• TNBC (UW_OvCa_RNASeq) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002524

• TNBC (UW_OvCa_WGS) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002544

• Director of the Institute of Reproductive Genetics, Münster, Germany

  Dac EGAC00001002589

• TNBC (COH_WGS) - Data Access Committee at The Jackson laboratory

  Dac EGAC00001002574

• Data access commitee at the Molecular Exercise Physiology group

  Dac EGAC00001002606

• The Genomic Landscape of Prostate Cancer Brain Metastases

  Study EGAS00001004557

• Developmental Maturation of Hematopoietic Stem and Progenitor Cells Mediated by Lin28b/Let-7/Cbx2

  This study encompasses two human cell lines used to profile polycomb repressive complex markers during hematopoietic maturation.  This study includes epigenomic mark sequencing data obtained via the CUT&RUN protocol.

  Study phs002507

• Exome Recapture and Sequencing of Prospectively Characterized Clinical Specimens From Cancer Patients

  The study cohort comprises samples from patients whose tumors have been prospectively characterized as part of their care at Memorial Sloan Kettering Cancer Center. This includes a variety of distinct tumor type and molecular subtypes.

  Study phs001783

• Whole-exome-sequencing and Whole-genome-sequencing and RNA-sequencing in Familial amyotrophic lateral sclerosis (ALS)

  To identify the genetic cause and modifiers of Familial amyotrophic lateral sclerosis (ALS), we performed Whole-exome-sequencing and Whole-genome-sequencing and RNA-sequencing of Familial amyotrophic lateral sclerosis (ALS) patients.

  Study JGAS000358

• Bisulfite sequencing of cell-free DNA in NMOSD patients

  Cell-free DNA was extracted from plasma and analyzed by bisulfite sequencing in Neuromyelitis Optica Spectrum Disorders(NMOSD) patients and healthy controls(HC). we aimed to investigate the primary source of cell-free DNA production.

  Study JGAS000515

• Paired primary and recurrent patient GBM sample EZH2 binding profiles

  To ascertain the change in PRC2 occupancy at different promoter sets between primary and recurrent tumour, we performed EZH2 ChIPseq in longitudinal GBM samples from one Up and one Down responder from our cohort.

  Study EGAS50000000100

• CSF and PBMC scRNAseq RRMS patients at diagnostic n=5

  To get insights about immune cells infiltrating cells the CSF of RRMS patients (n=5), we proceed to 10X scRNAseq of paired CSF and blood circulating cells (about 20000 cells each) sampled at diagnostic.

  Study EGAS50000000308

• Brazilian Genomes

  We generated 2,723 high-coverage whole-genome sequences of Brazilian population from the country’s five geographical regions. This diverse group encompasses individuals from urban and rural settings (including riverine communities) and represents various ethnic backgrounds, including Afro-Brazilians.

  Study EGAS50000000730

• 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

• Multi-omic single-nucleus ATAC-seq + RNA-seq of nuclei from the motor cortex of ALS/ALS-FTD patients and unaffected controls

  A multi-omic dataset of single-nucleus paired ATAC-seq + RNA-seq data of nuclei from the post-mortem human primary motor cortex from patients with ALS/ALS-FTD and unaffected controls.

  Dataset EGAD50000002240

• Whole exome sequence of human XXY fibroblasts

  This dataset contains Whole exome sequence generated using human skin fibroblast sample (ID 419281) from Klinefelter XXY syndrome patient fibroblasts. These fibroblasts were used to generate autosomally isogenic human iPSCs. The sample DNA was collected using commercial kit and Human All Exon v5 capture paired library was sequenced using Illumina HiSeq device. The fastq file (ID 493224) and analysis (ID 3209) bam files have been deposited.

  Dataset EGAD50000001362

• RNA-seq

  RNA sequencing files that were used in our study. The cohort was composed of 39 cases of RNA sequencing data. RNA-seq library was prepared with rRNA depletion method, and the sequence was performed using DNBSEQ sequencer.

  Dataset EGAD50000000971

• Metadata Submission

  Metadata Submission Welcome to the EGA Metadata Submission landing page. Here, we provide you with essential resources to facilitate a seamless submission process. Before starting your submission, please make sure you check the following pages: Submission FAQ Submission Quickguide Submission account terms EGA metadata schema If you want to submit sequencing and/or phenotypic data check these pages: Submitter Portal Submitter Portal API If you want to submit array data check these pages: Array documentation Webin Webin API

  Documentation submission/metadata/submission

• Breast Cancer PDTX Encyclopaedia

  Molecular data from the collection of PDTX breast cancer models described in Bruna et al, 2016. Cell. It includes whole exome sequencing, shallow whole genome sequencing, expression arrays and reduced bisulfite representation sequencing (RRBS).

  Study EGAS00001001913

• Genomic characterization of NUT midline carcinoma

  In this study, we sequenced two NUT midline carcinoma genomes. Analysis of rearrangement breakpoint provided information on the generating event of BRD-NUT rearrangements. Mutational signature analysis also revealed biological process during tumorigenesis of NUT midline carcinomas.

  Study EGAS00001001934

• Metastatic_Breast_Cancer_Whole_Genome

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

  Study EGAS00001000902

• BASIS_RNAseq

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve 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 EGAS00001000707

• Breast_Cancer_FRT_RNA_seq

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000420

• Balanced_Ependymoma

  We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Study EGAS00001000174

• (h)MeDIP-Seq of high-risk prostate cancer

  Immunoprecipitation of methylated and hydroxymethylated DNA was performed on DNA isolated from tumoral and non-tumoral prostate tissue of patients with high-risk disease. Samples were sequenced on the Illumina HiSeq as 50 bp single end.

  Study EGAS00001001019

• Breast_Cancer_Whole_Genome_Sequencing

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve 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 EGAS00001000210

• Triple_Negative_Breast_Cancer_RNA_Sequencing

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

  Study EGAS00001000377

• Blueprint RNAseq profile of purified plasma cells from multiple myeloma patients and tonsils of healthy donors

  In the context of an epigenomic study of multiple myeloma, a have generated RNAseq profiles of purified plasma cells from 11 multiple myeloma patients and tonsils of 4 healthy donors

  Study EGAS00001001110

• BCL11B enhancer hijacking defines a subtype of lineage ambiguous stem cell leukemia

  Hijacking of primitive hematopoietic enhancers, or generation of a neo-enhancer by genomic amplification, results in deregulation of BCL11B as the defining feature of a subset of T/myeloid leukemia

  Study EGAS00001004810

• GWAS in bullous pemphigoid in Germans

  Genome-wide association study of bullous pemphigoid in Germans, using 446 BP patients and 433 age- and sex- matched controls. 6 SNPs in the HLA locus were found to be of genome-wide significance.

  Study EGAS00001004627

• RNA Sequencing of Colorectal Liver Metastases

  Reverse-stranded paired-end 75 base-pair RNA sequencing libraries of 93 metastatic FFPE samples were constructed using Illumina Total RNA Stranded Kits. Ribosomal RNAs (rRNAs) were depleted by using the Ribo-Zero rRNA Removal Kit (Illumina). Libraries were sequenced on a HiSEQ2500 machine. Five samples were re-sequenced using paired-end 50 base-pair libraries due to the smaller insert sizes.

  Dataset EGAD00001004111

• Deciphering RBP - alternative splicing networks in ALS iPSC-MN: TDP-43, NOVA1, NOVA2 and RBFOX2 eCLIP-seq

  We produced enhanced cross-linking immunoprecipitation (eCLIP) sequencing data of the RNA binding proteins (RBP) TDP-43, NOVA1, NOVA2 and RBFOX2 in iPSC motor neurons of two healthy control individuals, respectively.

  Study EGAS00001005880

• TB-DAR Genotyping Study

  Active TB patients (sputum smear-positive and GeneXpert-positive) recruited at the Temeke District Hospital in Dar es Salaam, Tanzania, as part of a prospective study that ran between November 2013 and June 2022 (TB-DAR cohort).

  Study EGAS00001007216

• Molecular programs of melanoma brain metastases (MBM)

  We performed paired-end whole transcriptome sequencing of fresh frozen or intraoperative brain metastases of therapeutically treated stage IV melanoma patients. In addition, we analysed the epigenetic landscape of tumors usind Illumina 850k bead chip technology.

  Study EGAS00001005976

• Genomic Rearrangements in Pediatric Cancer

  This study contains a collection of samples used to determine the role and impact of genomic rearrangements in a pan cancer pediatric cohort.

  Study EGAS00001005312

• Paired-WGS-two-families-with-GBA-variants-and-Parkinsons-disease

  We performed whole- genome sequencing, rare variant filtering, segregation analysis and functional validation of PD cosegregating rare genetic variation in two families (6 samples) segregating PD associated GBA variants c.115+1G>A (ClinVar ID: 93445, ) and p.L444P (ClinVar ID: 4288) respectively. The paired WGS sequencing was run on HiSeq X Ten and the library preparation kit was Illumina TruSeq DNA nano.

  Dataset EGAD00001006561

• RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  Dataset EGAD00001001944

• Single nucleus RNA sequencing of isolated NK cells and CD56+ T cells from digested NSCLC tumor lesions

  In order to explore the intratumoral NK cell heterogeneity at a transcriptomic level, we performed matched single nucleus RNA sequencing of isolated CD45+CD3+CD56+ immune cells from 11 NSCLC patients.

  Study EGAS50000001189

• Single nucleus ATAC sequencing of isolated NK cells and CD56+ T cells from digested NSCLC tumor lesions

  In order to explore the intratumoral NK cell heterogeneity at an epigenetic level, we performed matched single nucleus ATAC sequencing of isolated CD45+CD3+CD56+ immune cells from 11 NSCLC patients.

  Study EGAS50000001190

• Whole-exome sequencing of P2RY8-CRLF2-positive ALL on Illumina HiSeq 2000, 100 bp paired-end

  Genomic DNA from leukemic and remission bone marrow mononuclear cells was isolated with the QIAamp DNA Blood Extraction Kit (Qiagen, Venlo, The Netherlands). Libraries were prepared using Nextera Rapid Capture Exome Kit (Illumina, San Diego, USA). Paired-end sequencing of 100 bp reads was performed on a HiSeq 2000 (Illumina) to obtain at least a 50 x coverage.

  Dataset EGAD00001002666