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• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10345i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003107

• Immunotesting cohort with RNA-seq data of melanoma samples

  This dataset contains RNA-seq raw data in fastq format from 9 melanoma samples. The samples are formalin-fixed paraffin-embedded (FFPE) treated. For target enrichment SureSelect XT Human All Exon V6 was used. The libraries were sequenced in paired-end mode (2 x 50 nt) on a NovaSeq6000 S2 flow cell.

  Dataset EGAD00001006783

• MET amplification in gastric cancer

  WES sequencing of two cases of MET amplified gastric cancer. Six unfixed fresh frozen samples were obtained from the primary tumors (three samples from each) and three samples from corresponding non-neoplastic mucosa. In addition, formalin-fixed and paraffin-embedded (FFPE) samples were obtained from the primary tumors (n=2), lymph node metastases (n=7) and non-neoplastic mucosa (n=2).

  Dataset EGAD50000001099

• Aging and viral evolution impair immunity against dominant pan-coronavirus-reactive T cell epitope

  In this project we have analysed gene expression and Tcell repertoires of CD40L+41bb+ and CD40L-41bb- Tcells from young and old donors after stimulation with the iCope peptide.

  Study EGAS50000001150

• Segmental_cherry_angioma_case

  Cherry angiomas are common benign blood vessel growths on the skin. In this study we characterise mutational profile of a cherry angioma and adjacent skin biopsied from a patient with multiple lesions with segmental presentation.

  Study EGAS00001008212

• Fibromyalgia versus small fiber neuropathy: Diverse keratinocyte transcriptome signature

  We provide a diverse keratinocyte transcriptome signature between SFN and FMS patients, which may hint towards distinct pathomechanisms of small fiber sensitization and lay the basis for advanced diagnostics in both entities

  Study EGAS00001005004

• 666PG Whole genome alignment

  Aligned whole genome sequences in this dataset are from CPCG-GENE Normal/Tumor pairs used in the 666PG study. Raw sequences data was aligned against the human reference (GRCh37 + decoy) using bwa-mem and GATK for indel-realignment and recalibration

  Dataset EGAD00001004957

• scRNAseq data of scrambled and siRNA-mediated knock-down of the minor spliceosome snRNA U6atac

  scRNAseq data of scrambled and siRNA-mediated knock-down (96h) of the minor spliceosome snRNA U6atac in androgen-sensitive LNCaP cells and in patient derived neuroendocrine organoids (PM154). Three replicates for each cell line.

  Dataset EGAD00001007996

• HiC (chromosomal conformation capture) data for Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

  This dataset contains chromosomal conformation capture data from fourteen samples (eleven tumor samples and three tumor derived cell lines). Libraries were prepared using the Illumina TruSeq LT sequencing adaptors. Sequencing was performed on the HiSeq X or NovaSeq platforms resulting in 28 FASTQ files.

  Dataset EGAD00001008801

• Post Mortem brain data used in paper "Significant and pervasive effects of RNA degradation on Nanopore direct RNA sequencing"

  This dataset contains data used in the paper titled "Significant and pervasive effects of RNA degradation on Nanopore direct RNA sequencing. The data consists of one post mortem sample that was sequenced with direct RNA sequencing form Oxford Nanopore Technologies on a promethION flow cell.

  Dataset EGAD00001009308

• Ovarian Carcinosarcoma DNA and RNA sequencing of patient samples in the UK cohort.

  Ovarian Carcinosarcoma DNA and RNA sequencing of patient samples in the UK cohort (n=18).

  Dataset EGAD00001011068

• Picuris Pueblo Genomic Project (Ancient Data)

  Data Access Committee for the ancient dataset of the project "Picuris Pueblo oral history and genomics reveal continuity in US Southwest".

  Dac EGAC50000000525

• EpiMatch_DNA_Methylation_Resource

  Genome-wide DNA Methylation Data from Illumina HumanMethylationEPIC arrays for whole blood samples from 403 healthy individuals. Additional raw data (IDAT files) and associated phenotype information are available for all individuals included in this study (n=570) directly from CIBMTR. Data are available under controlled access release upon reasonable request and execution of a data use agreement. Requests should be submitted to CIBMTR at info-request@mcw.edu and include the study reference IB17-04

  Dataset EGAD00010002283

• Whole-exome sequencing of hepatocellular carcinoma biopsies

  All 122 HCC biopsies and 115 non-tumoral tissues from 114 patients were subjected to whole-exome sequencing. Whole-exome capture was performed using the SureSelectXT Clinical Research Exome (Agilent Technologies) or SureSelect Human All Exon V6+COSMIC (Agilent Technologies) platforms according to the manufacturer’s guidelines. Sequencing was performed on an Illumina HiSeq 2500 at the Genomics Facility Basel according to the manufacturer’s guidelines. Paired-end 101-bp reads were generated.

  Dataset EGAD00001008182

• Integrative_Oncogenomics_of_multiple_myeloma

  We used targeted capture and massively parallel sequencing of exomes of CD138 purified plasma cells and matched somatic DNA from 17 patients with Multiple Myeloma. For each patient, an early tumor sample (at diagnosis) and a late one (at relapse) were available. For few of them, an additional late sample (2nd progression) was present. In total, the study has 52 samples. 1044 variants were validated by 454 sequencing. The present study will validate an additional 4630 variants by targeted pull-down and sequencing. All 52 samples will be indexed and then will be pre-pooled in groups of 5 or 6. The sequence capture will use 10 reactions. All samples will then be pooled and go thorugh one lane of HiSeq.

  Study EGAS00001000244

• Sequencing of an organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity.

  Kidney tumors are among the most common solid tumors in children, comprising several distinct subtypes differing in many aspects, including cell-of-origin, genetics, and pathology. Pre-clinical cell models capturing the disease heterogeneity are currently lacking. Here, we describe the first pediatric cancer organoid biobank. It contains tumor and matching normal organoids from over 50 children with different subtypes of kidney cancer, including Wilms tumors, malignant rhabdoid tumors, renal cell carcinomas, and congenital mesoblastic nephromas. The malignant rhabdoid tumor organoids represent the first organoid model for tumors of non-epithelial origin. The tumor organoids retain key properties of native tumors, useful for revealing patient specific drug vulnerabilities. We further demonstrate that organoid cultures derived from Wilms tumors consist of multiple different cell types, including epithelial, stromal and blastemal-like. Our organoid biobank captures the cellular heterogeneity of pediatric kidney tumors, providing a representative collection of well-characterized models for basic cancer research, drug-screening, and personalized medicine.

  Study EGAS00001003853

• Genetic background for cardio vascular disorders in the general Finnish population

  Low coverage (4-6x) sequencing on samples from population cohorts (Finrisk, Health2000) will be done at Wellcome Trust Sanger Institute (WTSI) using Illumina HiSeq sequencing technology. We will produce 100bp paired end reads. Variants will be called using the 1000 Genomes Project pipeline. The samples have been selected from a national representative set of approximately 30,300 samples and comprises 500 individuals of each gender in the extreme tail of high density lipoprotein (HDL) concentrations. Included individuals were between 25 and 65 years of age. Individuals with a diagnosis of diabetes or BMI>30 were excluded from the study.

  Dataset EGAD00001001251

• Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

  We tested the efficiency and reproducibility of 10 RNA isolation methods on 5 different biofluids. Pooled human plasma and serum, bile and urine were used along with cell culture supernatants from human embryonic stem cells (hESC), primary neonatal rat ventricular myocytes (NRVM) and human cholangiocarcinoma cells (KMBC). 4 RNA isolation methods designed to isolate total RNA from bio fluids without enrichment of exRNA carriers were used. 6 methods that preferentially enriched for exRNA carriers were also compared. Small RNA libraries were constructed using the NEBNext small-RNA library prep. The efficiency and reproducibility of the different RNA isolation methods was compared using small-RNA seq.

  Study phs002143

• Massachusetts General Hospital/Eisai National Institute of Mental Health (NIMH) Genetics Initiative Alzheimer's Disease GWAS - Affymetrix GeneChip Human Mapping 500K Array Set

  This study cohort was collected as part of the National Institute of Mental Health (NIMH) Alzheimer's disease Genetics Initiative Study. Recruitment of families, predominantly sibling, for the cohort was focused on local memory disorder clinics, nursing homes, and the surrounding community. Clinical evaluation was performed at the University of Alabama at Birmingham, Johns Hopkins University, and Massachusetts General Hospital/Harvard Medical School. Informed consent was obtained from all study participants, for participants with extensive cognitive impairment, a legal guardian or caregiver with power of attorney provided consent. To determine age of onset, a creditable informer was interviewed and medical records were evaluated.

  Study phs000483

• RNAseq of GEPARSIXTO

  294 formalin-fixed paraffin-embedded (FFPE) tissue samples were sent to the UNC Lineberger Comprehensive Cancer Center Translational Genomics Lab (TGL) for RNA isolation using the Maxwell 16 MDx Instrument (Promega AS3000) and the Maxwell 16 LEV RNA FFPE Kit (Promega AS1260) following the manufacturer’s protocol (Promega 9FB167). 279 total RNA sequencing libraries were prepared at TGL using a Bravo Automated Liquid-Handling Platform (Agilent G5562A) and the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina 20020599) following the manufacturer’s protocol (Illumina 1000000040499). RNAseq library quality and quantity were measured using a TapeStation 4200 (Agilent G2991AA) and Qubit 3.0 fluorometer (Life Technologies Q33216), pooled at equal molar ratios, and denatured following the manufacturer’s protocol (Illumina 1000000106351). 271 total RNA sequencing libraries were sequenced at TGL on NovaSeq 6000 (Illumina 20012850) S4 flow cells (Illumina 20028313) following the manufacturer’s protocol (Illumina 1000000019358) using a 2x50 bp paired-end configuration and pool sizes of 91 libraries to target a read depth of 110 million clusters per library on average.

  Dataset EGAD00001010201

• Genome Dynamics in the Immune system lab-imagine

  Dac EGAC00001001254

• DAC Genetic variability in the glucocorticoid receptor NR3C1

  Dac EGAC00001002382

• B and T Cell Determinants of Influenza Vaccine Responses in the Elderly

  The study sequenced antibody heavy chain gene rearrangements from human subjects receiving influenza vaccination.

  Study phs000666

• Dataset for the "Study on the proliferation history of colorectal adenomas"

  Targeted genome sequences of the human X chromosome in 4 colorectal adenomas and 4 matched normal tissues from male patients

  Dataset EGAD00001000882

• Therapeutic vulnerabilities in the DNA damage response for the treatment of ATRX mutant neuroblastoma

  Whole genome sequencing of ATRX / TP53 knockdown clones of the neuroblastoma cell line SK-N-SH

  Study EGAS00001004550