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• 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

• Hi-C of human acute leukemias and healthy donors

  Hi-C of 17 primary samples obtained from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). Moreover, Hi-C of CD34+ HSPCs from 3 healthy donors are included.

  Dataset EGAD00001011051

• Gene panel sequencing of paired samples from primary and relapsed IDH-wt glioblastomas

  This dataset contains gene panel sequencing data from 43 sample pairs of primary and relapsed IDH-wt glioblastomas. The gene panel covers 50 glioma-associated genes. 14 of the sequenced sample pairs were sequenced with whole genome sequencing also and are accessible under EGAD00001004563.

  Dataset EGAD00001004565

• Whole-exome sequencing of rare autoimmune-related phenotypes

  We aim to whole-exome sequence DNA samples from 75 individuals with severe forms of Inflammatory Bowel Disease and related autoimmune diseases to identify the rare, highly penetrant, variants that we believe underlie these phenotypes. Case samples will be obtained from both new and existing (UK IBD Genetics Consortium) collaborators to ensure only the most extreme cases are sequenced.

  Dataset EGAD00001000408

• MutWP5: CRUK Mutographs of Cancer: Lung: PD43291_Novaseq (WG)

  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 2023-03-08.

  Dataset EGAD00001010111

• Res1_H23_exp2_MC_13.07.22

  8 samples are cell pellets for genomic DNA extraction. CRISPR PCR1 and PCR2 indexing - Please use standard Kosuke primers.

  Dataset EGAD00001012234

• Dataset of the transcriptomic profiling of skin biopsies from 221 psoriasis patients following treatment with Zasocitinib

  This dataset contains the paired fastq files generated from 221 samples collected from patients with moderate-to-severe plaque psoriasis and sequenced on the Illumina NovaSeq 6000 platform. Patients were randomized in a 1:1:1:1:1 ratio to receive oral Zasocitinib at doses of 2 mg, 5 mg, 15 mg, 30 mg, or placebo once daily for 12 weeks. Clinical response was defined as achieving a PASI 75 response at week 12, while histologic response was defined as the absence of KRT16-positive cells in lesional skin after 12 weeks of treatment.

  Dataset EGAD50000002224

• Amplicon based re-sequencing of multi-region PDAC samples

  Multi-region tumor samples were cut from frozen sections or FFPEs and reviewed from microdissection and H&E staining in order to select ones with high cellularity. DNA extraction was done using DNeasy Blood & Tissue Kits for frozen samples following the manufacturer’s guideline. Extracted DNAs were processed on an Illumina HiSeq 2500 in a paired end mode (100x100) using a custom targeted panel based on the list of all unique somatic mutations from the original WES data by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center (New York, NY).

  Dataset EGAD50000000354

• Fecal Microbiota Transplantation for refractory immune checkpoint inhibitor-associated colitis

  We report the first case series of ICI associated colitis successfully treated with fecal microbiota transplantation (FMT), with reconstitution of the gut microbiome and a relative increase in the proportion of regulatory T cells (Tregs) within the colonic mucosa. These preliminary data provide evidence that modulation of the gut microbiome may abrogate ICI-associated colitis.

  Study EGAS00001003217

• Whole genome sequencing data for Molecular Characterization of ETMRs

  This dataset contains whole genome sequencing data from 59 samples. WGS libraries were prepared using the Illumina TruSeq Nano DNA LT Library Prep or TruSeq Nano DNA HT Library Prep Kit following the manufacturer’s instructions. In brief, 100 ng of genomic DNA was fragmented to approximately 350 bp using a Covaris ultrasonicator (Covaris). The fragmented DNA was then end-repaired, size-selected using magnetic beads, extended with an ‘A’ base on the 3′ end and ligated with TruSeq paired-end indexing adapters. Up to four lanes per sample have been sequenced resulting in 222 Fastq files (paired end).

  Dataset EGAD00001006211