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• Whole Exome Sequencing of Bipolar cases, matched controls at Broad Inst on cohort from Cambridge, UK

  This research project was a collaboration between Cambridge University, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 2,873 Bipolar case/control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing cram files

  Dataset EGAD50000000627

• Single-cell transcriptomics of neuroblastoma tumors

  Single-cell RNA-sequencing (CITE-seq) and single-nucleus RNA-sequencing data were generated from neuroblastoma patient tumors to uncover transcriptional heterogeneity at a single-cell resolution. In addition, we used the data to validate our findings of the NBAtlas.

  Study EGAS50000000223

• RNA sequencing of Ewing and CIC-DUX4 sarcoma tumoroid models

  Tumoroid models from Ewing sarcoma and CIC-DUX4 sarcoma models were generated from patient tumor biopsies. Tumoroids were established in 3D matrigel domes and then propagated on a matrige layer. RNA sequencing was performed with established tumoroid models.

  Study EGAS50000000380

• Whole exome sequencing of Ewing and CIC-DUX4 sarcoma tumoroid models

  Tumoroid models from Ewing sarcoma and CIC-DUX4 sarcoma models were generated from patient tumor biopsies. Tumoroids were established in 3D matrigel domes and then propagated on a matrige layer. Whole exome sequencing was performed with established tumoroid models.

  Study EGAS50000000379

• Colorectal cancer functional annotation - MPRA

  We performed a Massively Parallel Reporter Assay (MPRA) in colorectal cancer (CRC) cell lines HT29 and SW403 and normal colon cell line HCEC-1CT. We specifically targeted the regions around the CRC GWAS loci to identify which variants alter transcription.

  Study EGAS50000000406

• Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.

  Whole exome sequencing was performed from 108 Diffuse Large B Cell Lymphoma samples (99 FFPE tumor tissue derived DNA and 9 circulating tumor DNA) and corresponding germline DNA of 38 controls. A library containing whole exome regions was used to isolate the DNA for sequencing (SureSelect XT Human All Exon V6 (Agilent technologies)). Sequencing on a NovaSeq 6000 instrument (Illumina, paired end, 2x100, mean 566Gb per FlowCell) was performed.

  Dac EGAC50000000261

• TIRE-seq_PDN

  TIRE-seq is a novel RNA sequencing method that integrates mRNA purification directly into library preparation, eliminating separate RNA extraction. The technique demonstrated utility across three biological applications, including capturing transcriptional changes in human T cells, identifying genes driving murine dendritic cell differentiation, and analyzing the dose-response effects of temozolomide on patient-derived neurospheres. With its simplified approach and high sequencing efficiency, TIRE-seq offers a cost-effective solution for large-scale gene expression studies.

  Dataset EGAD50000001261

• Whole-exome sequencing of tumor samples

  Whole exome sequencing of DNA samples from tumor samples of patients in the Neo-Pembro trial. For each patient, up to four samples were sequenced; one tumor biopsy at baseline, one tumor biopsy after induction chemotherapy, a tumor sample from resection material at cytoreductive surgery, and a reference normal DNA sample isolated from whole blood. DNA was obtained from fresh-frozen samples where possible, or formalin-fixed paraffin-embedded when no fresh-frozen sample was available.

  Dataset EGAD50000001150

• IgM VDJ repertoire sequencing of 3 healthy donors using 8 different PCR conditions

  Peripheral blood mononuclear cells (PBMCs) were sampled from 3 healthy donors to sequence IgM heavy chain V(D)J repertoire libraries. Libraries were generated by targeting IgM heavy chain V(D)Js with a 5’MTPX primerset and sequenced on an Illumina MiSeq machine. Each donor was sequenced 8 times, varying only PCR amplification conditions, for a total of 24 sequencing libraries and therefore 48 paired-end fastq files.

  Dataset EGAD50000001510

• Targeted RNA-Seq

  This dataset contains targeted RNA-Seq generated with the Illumina RNA Pan-Cancer panel. It comprises 2200 cancers from children and adults. The cancers represent a wide range of CNS, solid and haematopoietic tumours. Samples are from pathology specimens including FFPE, fresh frozen, bone marrow aspirate and peripheral blood. Samples were tested in a clinical diagnostic lab to identify relevant SNVs, indels and gene fusions.

  Dataset EGAD50000000980