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• Single-cell RNA-seq of matched pediatric AML tumors

  Single-cell RNA-seq of pediatric AML tumours from patients enrolled in the clinical trial AAML1031. Obtained using the 10X Chromium Single Cell 3’ Reagent Kit, v3.0. A total of 75 samples were obtained from biopsies at diagnosis, remission and relapse from 28 patients.

  Dataset EGAD00001011195

• RNA sequencing of control OM cells exposed to traffic-related air pollutants

  Total RNA sequencing of olfactory mucosa (OM) cells derived from cognitively healthy individuals exposed to traffic-related ultrafine particles (UFPs) for 24h and 72h in submerged cultures. The UFPs used for exposures were: A0, A20 and Euro6. Exposures were compared to the corresponding blank samples.

  Dataset EGAD00001011317

• Single-cell ATAC-seq of matched pediatric AML tumors

  Single-cell ATAC-seq of pediatric AML tumours from patients enrolled in the clinical trial AAML1031. Obtained using the 10X Chromium NextGEM Single Cell ATAC Reagent Kit, v1.1. A total of 64 samples were obtained from biopsies at diagnosis, remission and relapse from 25 patients.

  Dataset EGAD00001011194

• Single cell TCR Analysis of regulatory Tcells from blood, fat and skin

  Regulatory Tcells were FACS sorted and processed with 10x Genomics Chromium Next GEM SingleCell V(D)J Reagents Kits v1.1 sequencing. In total 17 samples were processed. Fastq files are supplied.

  Dataset EGAD00001007661

• Understanding the multicellular dynamics of clear cell renal cell carcinoma - spatial transcriptomics

  The dataset comprises of transcriptomes of tissue sections derived from either the tumour normal interface or tumour core from clear cell renal cell carcinomas. 16 sections are sampled in total using 10x Genomics' Visium technology.

  Dataset EGAD00001008781

• Processed DNA methylome sequencing data

  The dataset contains methylation values of all SNP-filtered CpG sites for all samples from the air pollution study (total n=60). Nasal lavage samples were collected from n=29 moderately exposed (residing in Stuttgart) and n=31 lowly exposed (residing in Simmerath) individuals. For methods and study details, please see PMID 37343754.

  Dataset EGAD00001011208

• ChIP-sequencing in human monocyte differentiation

  This dataset consists of ChIP-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. ChIP-sequencing was done for H3K27, RAD21 and CTCF. In total, the data set includes 120 samples.

  Dataset EGAD00001007954

• HiC-sequencing in human monocyte differentiation

  This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.

  Dataset EGAD00001007955

• Gene expression in human monocyte differentiation

  This dataset consists of RNA-seq data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, it includes 63 samples.

  Dataset EGAD00001007956

• Mapping of runs back to samples for snRNASeq data

  Mapping of runs back to samples for PDN, PDO and TIS snRNASeq data. 4 sets of matched PDN, PDO and TIS samples (12 unique samples total) underwent pooled snRNASeq (Parse Biosciences). 2 sublibraries were created from this and sequenced at separate times

  Dataset EGAD00001015609

• Breast Cancer -Very young women with ER+ tumor

  Corresponding data set is composed of whole exome sequencing of Korean ER positive breast cancer under 35. This set provides 100 alignment files from normal-tumor paired whole exome sequencing of 50 patients. This is a part of total project data set.

  Dataset EGAD00001002256

• Alopecia and Vitiligo

  exome sequencing data captured with agilent v4 (71k) and sequenced on illumina technology. data from a total of 40 samples, of which 14 are vitiligo cases with familial history of vitiligo or immune disease, and the remaining are alopecia areata cases.

  Dataset EGAD00001005289

• RNA-Seq data for paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes'

  When available (25 primary MDS, 12 MDS/MPN, and 6 AML-MRC cases), high quality RNA (stranded-total) was submitted for RNA-seq. RNA was extracted from bulk myeloid cells which was used as the tumor population. Files uploaded are mapped BAM files.

  Dataset EGAD00001003782

• Sequencing data of primary uveal melanomas and their matched metastases

  We performed targeted DNA sequencing of primary uveal melanomas and their matched metastases from 35 patients, analyzing a total of 124 tissues. Sequencing was performed on an Illumina HiSeq 2500 instrument using a panel of 538 genes commonly involved in cancer. 124 BAM files were generated.

  Dataset EGAD00001004453

• Transcriptome sequencing of gingivo-buccal oral squamous cell carcinoma for integrative analysis: alterations in expression of genes attributable to methylation changes

  Gingivo-buccal oral squamous cell carcinoma (OSCC-GB) is the most common cancer among men in India and is associated with high mortality. Although OSCC-GB is known to be quite different from tongue cancer in its genomic presentation and its clinical behavior, it is treated identically as tongue cancer. Predictive markers of prognosis and therapy that are specific to OSCC-GB are, therefore, required. To achieve this, we have carried out transcriptome (n=72) profiling of paired tumor-normal tissues collected from OSCC-GB patients from India. RNA sequencing was performed on tumor and paired adjacent normal samples from 72 OSCC-GB patients. From each patient, total RNA was extracted from tumor and normal tissue samples using AllPrep DNA/RNA Mini Kit (QIAGEN). The quality and concentration of isolated total RNA were checked using Agilent 2100 Bioanalyzer and NanoDrop 2000 (Thermo Fisher Scientific). The OD260/OD280 ratio was ≥ 2 and RNA Integrity Number (RIN) was ≥ 7.0 for all sequenced samples. Ribosomal RNA (rRNA) was removed from the RNA samples, using Ribo-Zero Magnetic Kit (Epicentre). Sequencing libraries were prepared from rRNA depleted samples using TrueSeq RNA Sample Preparation Kit (Illumina). Each triplex cDNA library pool was sequenced as 100bp paired-end on HiSeq-2000 or HiSeq-2500 (Illumina). Protocols suggested by the manufacturers were used for all assays.

  Study EGAS00001003893

• Whole-exome sequencing and microRNA profiling predicted relapse risk of stage I lung adenocarcinomas for the study and all the datasets.

  This dataset contains PAIR files and processed somatic copy number alteration value for array CGH of stage I lung adenocarcinomas from Asian patients. In total, there are 111 patients and 222 samples, including 111 tumor samples and 111 adjacent normal samples.

  Dataset EGAD00010001902

• RNA Sequencing of AD OM cells exposed to traffic-related air pollutants

  Total RNA sequencing of olfactory mucosa (OM) cells derived from individuals diagnosed with Alzheimer's disease exposed to traffic-related ultrafine particles (UFPs) for 24-h and 72-h in submerged cultures. The UFPs used for exposures were: A0, A20 and Euro6. Exposures were compared to the corresponding blank samples.

  Dataset EGAD50000000648

• Saliva_Fulani_Database

  In total, 90 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). Saliva Fulani dataset includes individuals from the following populations: 30 individuals from Senegal_FulaniLinguere, 30 individuals from Mauritania_FulaniAssaba, and 30 individuals from Mali_FulaniInnerDelta.

  Dataset EGAD50000000653

• Methylation Array data for: Three-dimensional patient-derived models of glioblastoma retain intra-tumoral heterogeneity

  3 sets of matched patient-derived-organoids (PDOs),  -neurospheres (PDNs), and parent glioblastoma tissue (9 samples total) underwent methylation array analysis. 200ng of each sample DNA extracted via a commercial kit (Qiagen) and loaded onto the Illumina EPIC v2.0 array. Data is provided as raw red and green .idat files.

  Dataset EGAD00010002745

• Dicer and/or ADAR1 depleted HEK293-LGP2 cells

  This dataset includes bulk RNA-sequencing data from HEK293-L cells subjected to siRNA-mediated knockdown of Dicer and/or ADAR1. In total, 12 samples are included, representing four experimental groups with triplicate biological replicates. RNA was extracted using TRIzol according to standard protocols and sequenced on an Illumina NovaSeq 6000.

  Dataset EGAD50000002044

• Total NF1 sequence in the patients with neurofaibromatosis type1

  We analyzed whole NF1 gene region at DNA (including whole exon and intron sequences) and RNA (full length cDNA of leukocyte) level for 20 patients with neurofibromatosis type 1.

  Study JGAS000288

• Whole transcriptome sequencing of C1498 cells.

  The dataset contains raw data (FASTQ) of whole transcriptome sequencing of C1498 cells (n=1 sample). Libraries were prepared with the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina, San Diego, CA, USA) and and 100bp paired-end reads were generated on the NovaSeq 6000 Sequencing System (Illumina).

  Dataset EGAD50000002404

• Whole exome sequencing of patient derived cell lines

  Whole exome sequencing of 3 patients derived cell lines and patient blood (N = 6 samples), performed using Agillent SureSelect All Exon V5 and Illumina HiSeq 4000. Data is in raw fastq format (N = 10 fastq pairs, 20 files total), as some samples were split between two lanes.

  Dataset EGAD00001007738

• bulk RNA-Seq samples of CRC patients

  The dataset contains samples of 30 CRC patients (3 samples for each patient, tumor and 2 normal adjacent tissue sites, 90 samples in total). Dataset is composed by fastq file (paired end) type from bulk RNA-Seq.

  Dataset EGAD00001009635

• Common clonal origin of chronic myelomonocytic leukemia and B cell acute lymphoblastic leukemia in a patient with a germline CHEK2 variant

  Whole exome sequencing data obtained from sorted leukemic clones and a buccal swab as germline reference. The dataset contains raw sequencing data (paired-end reads) for 3 samples (2 leukemic, 1 buccal swab), for a total of 6 fastq files.

  Dataset EGAD00001007644

• Small molecule screen reveals synergy of cell cycle checkpoint kinase inhibitors with DNA-damaging chemotherapies in medulloblastoma (methylation dataset)

  human medulloblastoma xenograft isolated from mouse brain was frozen and genomic DNA or RNA was extracted. Bisulfite converted DNA was processed and hybridised to illumina EPIC or 450K arrays using standard protocols. RNAseq was performed on total RNA.

  Dataset EGAD00001006583

• Cold Ischemia Study Dataset

  A total of 54 samples derived from 9 patients and frozem in 6 timepoints (T0 - immediately after resection, T1 - 10 minutes after resection, T2 - 20 minutes after resection, T3 - 30 minutes after resection, T4 - 45 minutes after resection, T5 - 60 minutes after resection) to assess the impact of ischemia on gene expression.

  Dataset EGAD00001015661

• Single-cell RNA-seq of immune cells from Melanoma tumors (Li et al, 2018)

  Single-cell RNA-seq profiling of immune cells sorted from human Melanoma tumors (and several matching PBMC samples). Contains de-multiplexed FASTQ files per plate (MARS-seq amplification batch, total 204 samples) and also de-multiplexed FASTQ files of single-cell TCRb-seq.

  Dataset EGAD00001004497

• WXS files for paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes'

  Paired whole exome sequencing for 32 primary MDS, 14 MDS/MPN, and 8 AML-MRC cases (total = 54). Normal comparator genomic DNA was extracted from lymphocytes purified by flow cytometry. Bulk myeloid cells were used as a source of tumor gDNA. Files uploaded are mapped BAM files.

  Dataset EGAD00001003781

• RNA sequencing of Korean ER positive breast cancer females aged under 35 years old.

  Corresponding data set is composed of RNA sequencing of Korean ER positive breast cancer under 35 years old. This set provides 50 alignment files of 50 tumor samples. This is a part of total project data set.

  Dataset EGAD00001003243

• Osteosarcoma whole genome rearrangement screen

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from Osteosarcoma cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Dataset EGAD00001000368

• GSCAN GWAS Meta-analysis of Tobacco and Alcohol use (GSCAN-GWAS)

  This study was a meta-analysis of genome-wide association study (GWAS) of substance use across 1.2 million total participants with European ancestry (some phenotypes are based on fewer participants). The phenotypes were chosen to represent different stages and kinds of substance use from initiation (age of smoking initiation) to regular use (cigarettes per day and drinks per week) to cessation (smoking cessation). For each of those phenotypes, collaborators shared their GWAS summary statistics, which were then meta-analyzed using a method that incorporates into the meta-analytic weighting the sample size, allele frequency and imputation quality score.

  Study phs001809

• Whole Exome Sequencing of Uveal Melanoma

  Uveal melanoma is a rare form of melanoma that occurs in the eye and has no effective treatment once metastatic. To further characterize the genomic events driving uveal melanoma, whole exome sequencing was performed on 61 primary tumors derived from enucleations, 3 liver metasases, and paired normal DNA. Recurrent somatic genetic alterations including point mutations, small insertions and deletions, as well as copy number variations were identified. In addition, RNA sequencing of uveal melanoma cell lines expressing shRNAs was performed from total RNA as well as polysome-associated mRNA in order to identify transcripts regulated by EIF1AX at the level of translation.

  Study phs001370

• OCD Collaborative Genetic Association Study (OCGAS)

  The OCD Collaborative Genetics Association Study Group (OCGAS) was funded by NIMH to conduct a genome-wide association study to identify disease susceptibility loci of early-onset obsessive-compulsive disorder (OCD). Collaborators at Johns Hopkins, Brown, Columbia, MGH, UCLA, and NIMH evaluated 2,000 individuals with OCD and collected DNA from these individuals and both their parents. The genotyping and analyses was performed in two stages. In the first stage 1,065 families (comprising 1406 patients with OCD and 2895 individuals in total) were genotyped on the Illumina OmniExpress GWA (SNPs) panel at the JHU SNP Center.

  Study phs000903

• NHLBI TOPMed: Children's Health Study (CHS) Effects of Air Pollution on the Development of Obesity in Children (Meta-AIR)

  The Effects of Air Pollution on the Development of Obesity in Children (Meta-AIR) study was proposed to study a subset of the Children's Health Study (CHS) participants representing the extremes of long-term traffic-related air pollution exposure occurring in Southern California CHS communities. The primary aim of the Meta-AIR study was to investigate whether lifetime exposure to air pollution increases risk for obesity and metabolic dysfunction at 17-18 years of age. A total of 56 Hispanic White participants (16 asthma cases and 40 controls) were included in the TOPMed project.

  Study phs001604

• Merkel Cell Carcinoma Tissue and Data Repository

  Merkel cell carcinoma (MCC) is a rare, aggressive neuroendocrine skin cancer with increasing incidence in the United States. In this study we performed the first whole genome sequencing of three Merkel cell carcinomas with their matched normal tissues for somatic variant calling. From these data we describe the likely mechanism of Merkel cell polyomavirus integration and focal host genomic amplifications in two tumors and the dominance of UV-mediated mutagenesis in a virus-negative tumor. We also performed poly-A RNA sequencing on a total of six Merkel cell carcinomas to address expression differences between virus-positive and virus-negative MCC.

  Study phs002189

• Drug Perturbation of Primary Lymphoma Patient Samples and RNA Sequencing

  This submission contains 3'-end-based shallow-depth RNA sequencing data from 108 patients with chronic lymphocytic leukemia and 8 patients with lymphoma. Each primary patient sample was treated in vitro with DMSO as a control and with up to ten small-molecule drugs (ibrutinib, duvelisib, everolimus, trametinib, nutlin-3a, I-BET762, MK2206, selinexor, compound 26, and a combination of ibrutinib and compound 26). The samples were sequenced after 48 hours. The total data set consists of 1476 RNA sequencing samples from 6 batches (pilot, batch 1, batch 1 replicate, batch 2, batch 3, batch 4).

  Study EGAS50000001500

• RNA-seq analysis of megakaryocytes and granulocytes in Quebec platelet disorder

  Quebec Platelet disorder (QPD) is a unique bleeding disorder that markedly increases urokinase plasminogen activator (uPA) in megakaryocytes and platelets but not in plasma or urine. The cause is tandem duplication of a 77 kb region of chromosome 10 containing PLAU and C10orf55. Blood cells and cultured megakaryocytes from donors (7 QPD, 10 control subjects) were prepared for total and allele-specific, quantitative reverse transcription polymerase chain reaction, immunoassays, Western blots and RNA-seq. Transcriptomes for cultured megakaryocytes and peripheral blood granulocytes from 4 control and 3 QPD individuals were analyzed using mRNA-seq.

  Study EGAS00001001840

• Stage-specific gene and transcript dynamics in human male germ cells

  The testis is one of the most transcriptionallyactive organs, however how germ cell differentiation is controlled at the molecular level remains largely unknown. To study global transcriptional dynamics during human spermatogenesis we sequenced total RNA of human testicular biopsies with 5 specific histological phenotypes: Sertoli cell-only (SCO, n=3), spermatogenic arrests at the spermatogonial (SPG, n=4), spermatocyte (SPC, n=3), and spermatid (SPD, n=3) level, as well as normal spermatogenesis (Normal, n=3). To our knowledge, this work provides the most complete capture of the transcriptome and its dynamics during human spermatogenesis to date.

  Study EGAS00001006135

• TMD_AMKL_targeted_follow_up

  Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.

  Study EGAS00001000569

• TMD_AMKL_targeted_follow_up_part_2

  Genomic libraries will be generated from total genomic DNA derived from 200+ patients with childhood Transient Myeloproliferative Disorder (TMD) and or Acute Megakaryocytic Leukemia (AMKL) as well some matched constitutional samples (n < 50). Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 96 Samples will be individually barcoded and subjected to up to two lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.

  Study EGAS00001000732

• Single cell T cell Landscape and T Cell Receptor Repertoire Profiling of AML in Context of PD-1 Blockade Therapy

  Eight pretreatment and 14 posttreatment bone marrow (BM) aspirates from 8 patients with R/R AML treated with azacitidine and nivolumab along with 2 control BM from healthy donors were profiled with scRNA sequencing with matching scTCR -, scBCR - and scATAC sequencing. Additionally, the targeted DNA sequencing in at least 1 time point per patient (total evaluated 17/22 samples, two samples were performed using CLIA-certified molecular diagnostic assay and data is not available) was performed. The Fastq files and/or bam files are available in this dataset.

  Study EGAS00001004894

• Clinical utility of combined low-pass whole genome and targeted sequencing in liquid biopsies for diagnosis and monitoring of pediatric solid tumors

  We designed a liquid biopsy (LB) platform employing Low-Pass Whole Genome Sequencing (LP-WGS) and targeted sequencing of cell-free (cf) DNA isolated from plasma for detecting genome-wide copy number alterations and targeted gene fusions in pediatric solid tumors. A total of 143 plasma samples were analyzed from 19 controls (patients with non-oncologic diagnoses) and 73 patients, including 44 with bone or soft tissue sarcomas, 12 with renal tumors, 10 with germ cell tumors, 5 with hepatic tumors, and 2 with thyroid tumors.

  Study EGAS00001006913

• Neuroblastoma patient Total RNA Seq data

  Tumor Total RNA Seq data of primary neuroblastomas. This is an update of the „Berlin Neuroblastoma Dataset” (EGAS00001004022). This data was used for the analysis of circular RNA expression and regulation in neuroblastoma.

  Dataset EGAD00001008124

• Processed Total RNA Counts for the RNA Profiling from Indian HFrEF Cohort Dataset

  This dataset contains processed RNA count data for the 49 Heart Failure samples profiled by RNAseq for the Indian HFrEF Cohort from the study Integrated Transcriptomic and Regulatory RNA Profiling Reflects Complex Pathophysiology and Uncovers a Conserved Gene Signature in End Stage Heart Failure RNA-Seq data.

  Dataset EGAD50000001193

• EMBARCAM BC360 PROJECT

  This dataset is related to the EMBARCAM BC360 PROJECT. A total of 106 breast cancer samples, from Pregnancy-Associated Breast Cancer (PABC) (n=57) and non-PABC (n=49) patients, were analysed using the nCounter Breast Cancer 360 V2 panel on the NanoString platform. All samples were FFPE tumor samples from breast cancer patients, derived from GEICAM/2012-03, GEICAM/2017-07, and EpiGEICAM studies, sponsored by GEICAM.

  Dataset EGAD00010002709

• Dataset for Multiple Myeloma RNA data

  This dataset contains 371 case and control RNA sequencing samples of patients with multiple myeloma. Sequencing was performed on Illumina NovaSeq 6000 and HiSeq X, HiSeq 4000 and HiSeq 2000 using TruSeq Stranded RNA and TruSeq Stranded total mRNA Kits. The sequencing was always paired.

  Dataset EGAD50000000683

• ResolveCRPS study - Transcriptomics

  Transcriptome profiling of CRPS-affected skin using low-input total RNA-seq (paired-end mode with 54 and 68 nt read length for R1 and R2 respectively, Illumination NextSeq2000). 42 snap-frozen skin biopsies were analyzed together with longitudinal clinical data. The dataset contains FASTQ files, the processed read count matrix, and the corresponding clinical metadata.

  Dataset EGAD50000001545

• SNP Array data for: Three-dimensional patient-derived models of glioblastoma retain intra-tumoral heterogeneity

  4 sets of matched patient-derived-organoids (PDOs),  -neurospheres (PDNs), and parent glioblastoma tissue (12 samples total) underwent SNP array analysis. 200ng of each sample DNA extracted via a commercial kit (Qiagen) and loaded onto the Global Screening Array v2.0 array. Data is provided as raw red and green .idat files.

  Dataset EGAD00010002744

• Bulk 3' mRNA-Sequencing of human ASC-derived kidney tubuloids

  Bulk 3' mRNA-Seq raw files (FASTQ) from human kidney tubuloids derived from 4 separate donors in collagen-based dome culture and suspension culture. Samples were collected for sequencing on day 7 of passage 3, 4, and 5. Total = 24 samples.

  Dataset EGAD50000002335