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• Low Coverage Whole Genome Sequencing from high grade osteosarcoma

  This dataset contains the WGS of 35 samples (high grade osteosarcoma). All cases were reviewed by an expert bone pathologist and have a tumour content of 50% minimum. Paired-end libraries from fresh frozen tumour samples were prepared using the Agilent SureSelectXT HumanV5 kit for whole-genome sequencing (WGS). These were sequenced together with a tumour complementary DNA on an Illumina HiSeq2500 (paired-end 100 bp). Sequencing reads were mapped to the GRCh37 human reference genome using HISAT2

  Dataset EGAD00001006540

• Functional screening on patient-derived organoids identifies a therapeutic bispecific antibody that triggers EGFR degradation in LGR5+ tumor cells

  Patient-derived organoids (PDOs) have demonstrated predictive value in prospective clinical trials supporting selection of personalized treatments. Because PDOs retain the organization and physiological functions of their source tissue, PDO biobanks could also be an ideal substrate to screen for novel therapeutic interventions. Here we describe a large-scale functional screen of dual targeting bispecific antibodies (bAbs) on a colorectal cancer (CRC) PDO biobank to target their dependency on cancer stem cells. A novel drug discovery pipeline was assembled where therapeutic bAb panels generated against WNT and receptor tyrosine kinases (RTK) targets were functionally evaluated by high content imaging to capture the complexity of PDO responses across a wide range of different CRCs and paired normal colonic mucosa samples. Our strategy resulted in a bAb that specifically triggers EGFR degradation in LGR5+ CSCs and that exhibits unique therapeutic properties such as potent growth inhibition of KRAS mutant CRCs, blockade of metastasis initiation in preclinical models and minimal toxicity towards normal LGR5+ colon stem cells.

  Study EGAS00001004584

• Sequencing data for oesophageal and related samples - Alex Frankell et al (WGS)

  Data supporting: "The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic." Frankell et al. WGS (BAM files) 379 matched tumour-normal pairs

  Dataset EGAD00001004417

• Multidimensional and Longitudinal Immune Profiling of Sepsis in Uganda

  We conducted a prospective, observational cohort study of adults (RESERVE-U-2-TOR) admitted to Tororo General Hospital in eastern Uganda with severe, undifferentiated infection (i.e., suspected sepsis). Briefly, whole-blood samples were collected in PAXgene blood RNA tubes (PreAnalytiX, Qiagen, Germantown, MD, USA), from which RNA was extracted using PAXgene Blood RNA Kits (cat. no. 762164) (Qiagen). Sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina, after which libraries were multiplexed and sequenced on the Illumina NovaSeq X Plus platform (Illumina, Inc, San Diego, CA). Data from this study available through dbGaP include raw RNA-Seq data generated from whole-blood samples collected upon RESERVE-U-2-TOR study enrollment (N=274).

  Study phs003914

• RNA-Seq on OCIAML-22 Fractions

  The donor AML patient (unsorted) that was used to generate OCI-AML22 was expanded for the indicated number of days (Donor: 0 day, 12d: 12 days, 2m: 2 months, 3m: 3 months), then sorted for the indicated fraction (CD34p: CD34+; CD34m: CD34-, CD38m: CD38-, CD38m: CD38-).

  Study EGAS00001006512

• MutWP5: CRUK Mutographs of Cancer: Lung: PD38233 (WG) (2021-02-02)

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutation burden in different portions of the lung. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this portion of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006930

• MutWP5: CRUK Mutographs of Cancer: Lung: PD43291_Novaseq (Exome) (2021-02-02)

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutaiton burden in different portions of the lung. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this poriton of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006932

• IMpower133 processed RNA-seq data for genes utilized for cluster assignments

  This dataset contains log2(TPM + 1) for 271 tumor samples profiled by RNA-seq for the subset of genes used for validation of the NMF cluster assignments.

  Dataset EGAD00001006928

• The polarity and specificity of antiviral T lymphocyte responses determine susceptibility to SARS-CoV-2 infection in cancer patients and healthy individuals

  We monitored patient's anti SARS-CoV-2 immune responses using an in vitro cross presentation assay. The goal of this study was to identify immune correlates of clinical protection against SARS-CoV-2 infection. Briefly, peripheral blood mononuclear cells of patient were divided into a monocyte and lymphocyte. Monocyte were differentiated into monocyte derived dendritic (mo-DC)cells using GM-CSF and Interferon alpha. Mo-DC were then loaded with SARS-CoV-2 culture lysates , or VeroE86 lysates. SARS-CoV-2 loaded mo-DC were then used to stimulates their autologous lymphocytes and T cell cytokine secretion was monitored in the supernatant. We discriminated patients producing IL-2 and patients producing IL-5. RNA sequencing was performed for 18 patients, to identify gene profile associated with IL-2 or IL-5 production.

  Dataset EGAD00001008538

• Viral evasion Strategy for Generating Hypoimmunogenic hiPSC Lines

  Mismatches in HLA haplotypes between donors and recipients significantly increase the risk of graft failure due to immune rejection. To address these limitations, we introduced a cytomegalovirus-derived US2 encoding sequence into the AAVS1 safe-harbor locus of a human induced pluripotent stem cell (hiPSC) line. US2 expression in iPSC abolished HLA-A2 alloreactive T-cell activation without increasing NK cell degranulation, indicating preserved inhibitory signaling.

  Study EGAS50000001618