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• The Gut Microbiome of liver transplant recipients – Cross-sectional + Longitudinal (renal and liver)

  TransplantLines is designed as a single-center, prospective cohort study and biobank including all different types of solid organ transplant recipients as well as living organ donors. In the TransplantLines gut microbiome study the gut microbiome of solid organ transplant recipients is characterized and linked to clinical phenotypes. This batch contains the cross-sectional data from liver transplant recipients and longitudinal data from renal and liver transplant recipients.

  Study EGAS00001006258

• Novel Approach to High-Throughput Identification and Characterization of Neoantigens

  This study focuses on the development of novel approach for the screening, identification and characterization of neoantigen-specific T-cell receptors (TCRs). The developed method consists of collecting targeted RNA-Seq from a T-cell specific gene panel via 3' end Illumina sequencing combined to Oxford Nanopore based full-length TCR sequencing post T-cell activation. The data generated during this study demonstrates feasibility of the approach on a Jurkat control cell line as well as T-cells isolated from the blood of 3 independent healthy donors.

  Study phs002372

• Prime-seq of human term placenta-derived trophoblast organoids

  To study the one of the mechanisms through which obesity could affect placental cells, we used a novel microfluidic organs-on-a-chip device fabricated for co-culturing adipose spheroids and trophoblast organoids. The organoids were derived from the term placenta of a over-weight women. The adipose spheorids were derived from the white adipose tissue of a woman. And we sequenced the RNAs from the trophoblast organoids. The RNA extracted were subjective to Prime-seq library preparation protocol and being sequenced on Illumina NovaSeq 6000 at Novogene.

  Study EGAS50000000833

• Transcriptional effect of 4HTBZ on Caco-2 cells

  This study was performed to investigate the transcriptional effect of the H2S donor 4HTBZ on intestinal epithelial cells upon inflammatory stimulation. Caco-2/TC7 cells were pre-stimulated with interferon gamma (IFNG, 2.5 ng/mL) and tumor necrosis factor alpha (TNF, 10 ng/mL), followed by treatment with 4HTBZ (50 µM) or vehicle (0.1% DMSO) for 72 hours. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany), and cDNA libraries were prepared with the QuantSeq 3′ mRNA-Seq Kit (Lexogen, Inc.) and sequenced on an Illumina HiSeq4000 system.

  Study EGAS50000001237

• Accuracy and repeatability of epigenome-based signatures trained on Illumina MethylationEPIC BeadChip data

  Illumina DNA methylation microarrays are popular tools for discovering methylation patterns that enable epigenome-based trait prediction. To ensure reliable and accurate predictions, the robustness of the methylation assay is critical. This dataset comprises technical quadruplicate llumina MethylationEPIC (v1.0) data from matched cervical and blood samples, derived from four individuals, to evaluate the precision of methylation values and the repeatability of epigenome-based models trained to predict disease and aging. Fresh, and frozen blood were treated as separate tissue types, so the data stems from 4 * 4 * 3 = 48 microarrays.

  Study EGAS00001007184

• Targeted exome sequencing of pleomorphic invasive lobular carcinoma (PILC).

  Pleomorphic invasive lobular carcinoma (PILC) is an aggressive variant of invasive lobular breast cancer that is associated with poor clinical outcomes. Limited molecular data are available to explain the mechanistic basis for PILC behavior. To address this issue, we performed targeted sequencing using the Beijing Genomics Institute (BGI) TumorCare™ gene panel that includes 1053 genes that were selected based upon their association with cancer. This sequencing analysis identified genes that distinguish PILC from classic ILC (CILC) and invasive ductal carcinoma (IDC) by the incidence of their genomic changes.

  Study EGAS00001002871

• Single-cell RNA sequencing on 5063 single T cells isolated from peripheral blood, tumour and adjacent normal tissues from six hepatocellular carcinoma patients.

  Single-cell RNA sequencing on 5063 single T cells isolated from peripheral blood, tumour and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional properties of these individual cells, coupled with the assembled T cell receptor (TCR) sequences, were used to delineate the molecular subtypes, lineage, and functional properties of each T cell group. For five HCC patient, the exome-seq data of matched normal/tumor and bulk RNA-seq data of tumor are also available.

  Study EGAS00001002072

• Alignment BAM files and gene count files of the Illumina Sequencing Data (10 tumor samples)

  Reads were processed with the RNA-seq workflow 1.3.0 developed by the DKFZ Omics IT and Data Management Core Facility (https://github.com/DKFZ-ODCF/RNAseqWorkflow). First, FASTQ reads were aligned via two-pass alignment using STAR 2.5.3a. The STAR index was generated from the 1000 Genomes assembly and GENCODE Version 19 gene models with a sjdbOverhang of 200. Duplicate marking of the resultant main alignment file was done with sambamba 0.6.5. Gene-specific read counting was performed using featureCounts (from Subread 1.5.1) over exon features based on GENCODE Version 19 gene models. Both reads of a paired fragment were used for counting, and the quality threshold was set to 255, indicating that STAR found a unique alignment. Strand-specific counting was also used. For RPKM and TPM calculations, all genes on chromosomes X and Y, the mitochondrial genome, as well as rRNA and tRNA genes were omitted as they are likely to introduce library size estimation biases.

  Dataset EGAD00001008969

• Raw DNA and RNA data from breast cancer organoids, control samples and biopsies

  Whole genome sequencing data for primary tumors, matching control material from blood and their corresponding organoid. Whole transcriptome data for organoids.

  Dataset EGAD00001003751

• EGAD00010000628

  The TEENAGE study target population comprised adolescent students aged 13 to 15 years attending the first three classes of public secondary schools located in the wider Athens area of Attica.

  Dataset EGAD00010000628