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• RNA-seq and scRNA/TCR-seq data for publication: "Pharmacological inhibition of nonsense-mediated mRNA decay enhances anti-tumour immunity"

  RNA-seq and scRNA/TCR-seq data from patient-derived fragments (PDFs) analysed in publication by R. Vendramin, H. Fu, S. Fernandez Patel, Y. Zhao et al.

  Study EGAS50000001208

• Dataset for single cell transcriptome sequencing

  This datasets contains single cell transcriptome sequencing of 10 control samples. Sequencing has been performed on Illumina NovaSeq 6000 using 10xGenomics Chromium Next GEM Single Cell 5 Reagent Kits. Sequencing was always paired. This dataset additionally contains a .QS file from Seurat Analysis performed in R, generated as described in the related publication.

  Dataset EGAD50000001549

• ScRNA-seq of kidney organoids expressing different APOL1 variants and treated with IFN-γ

  This dataset includes scRNA-seq fastq files and Seurat counts and metadata for 3 samples of hiPSC-derived kidney organoid cells cultured in vitro in presence of IFN-γ. Samples were obtained from kidney organoids with APOL1 G1G1 variant, APOL1 G2G2 variant and an isogenic control.

  Dataset EGAD50000001743

• Synergy study: "Tissue resident CD8+ T cell clonal expansion in advanced triple negative breast cancer is associated with response to chemoimmunotherapy"

  Dataset of the study "Synergy study: "Tissue resident CD8+ T cell clonal expansion in advanced triple negative breast cancer is associated with response to chemoimmunotherapy". This dataset contains the cellranger's gene-expression matrices for the 5 prime single-cell RNA sequencing experiments

  Dataset EGAD50000000748

• RNA_TPO3_2023

  Human engineered CRC organoids (APC KO; KRAS G12D; TP53 KO) were grown in either glucose or lactate, in the presence and absence of DCA or BRD4 inhibition (JQ1). Samples were collected and processed for bulk RNA-seq.

  Dataset EGAD50000000089

• 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

• 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

• Predictor_ChemoNEAR_TNBC (2019-08-14)

  In this study a collection of core biopsies from breast cancer patients receiving neoadjuvant chemotherapy as part of the ChemoNEAR trial will be investigated. The study is intended to detect early acquired resistance in women with diagnosed breast carcinoma. Samples will undergo whole genome sequencing and analysis, including use of HR Predict. . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005255

• 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