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• WGS of exposed organoids

  The mutagenicity of bacteria was assessed by serially exposing human small intestinal organoids to various bacterial species or isolated toxins. We have used the following abbreviations: EWT: Organoids exposed to E. coli described in PMID: 32106218 EKO: Organoids exposed to isogenic E. coli as EWT, with knockout of the deltaClbQ gene, rendering them unable to produce colibactin DYE: Organoids exposed to FastGreen injection control dye NIS: Organoids exposed to E. coli Nissle ETBF: Organoids exposed to the protease toxin BTF produced by ETBF-bacteria.

  Dataset EGAD00001008687

• Single-cell sequencing of gammadelta and CD8+ alphabeta TCR sequences from blood and gut in coeliac disease

  Single-cell sequencing of gammadelta and CD8+ alphabeta TCR sequences from blood and gut in coeliac disease, before and during gluten challenge (Samples from baseline, day 6 and day 14 blood, and from baseline + day 14 gut). (Paired end, amplicon sequencing).

  Study EGAS00001004484

• Single-cell RNA-sequencing of peritoneal fluid from patients with achalasia

  The data published here contains single-cell RNA-sequencing (scRNAseq) data as obtained using the 3' scRNAseq using Chromium Single Cell 3’ Reagent from 10X Genomics on peritoneal fluid (PF) from patients with achalasia. Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000251

• Tumor mutational burden (TMB) calculated on bladder tumor pre-treatment DNA sequencing data

  Data from NABUCCO cohort 1 (NCT03387761). This dataset includes Tumor mutational burden (TMB) calculated on bladder tumor pre-treatment DNA sequencing data (n=24). Details about the Tumor Mutational Burden calculation can be found on the Methods section from the Nature Medicine paper (https://doi.org/10.1038/s41591-020-1085-z)

  Dataset EGAD00001006851

• LBC1921 fastq files

  297 members of the LBC1921 were sequenced using the Illumina HiSeq X platform. This dataset contains the fastq files.

  Dataset EGAD00001008775

• Immune deconvolution output

  Results of comprehensive immune deconvolution analysis through the TIMER2 web portal with algorithms specified in the publication.

  Dataset EGAD00001008789

• Whole genomes from Sahel

  The dataset includes 43 high coverge (30x) whole genome samples mostly from the Sahelian belt.

  Dataset EGAD00001011812

• Methylome profiling of epithelioid sarcoma

  Explore the methylome landscape of epithelioid sarcoma using array data.

  Study EGAS00001007257

• Infant_Spindle_Tumour_Study

  We aim to describe the transcriptomic landscape of infant spindle cell tumours.

  Study EGAS00001002935

• HCA_Muscle_Adult_Wellcome_RNA_Managed_Access

  Transcriptomic analysis of skeletal muscle, to understand the mechanisms of muscle ageing.

  Study EGAS00001007495