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• Bone marrow derived stromal cells from Myelodysplastic Syndromes

  In this study we performed exome sequencing of bone marrow derived, in-vitro expanded mesenchymal stromal cells from patients with Myelodysplastic Syndromes in order to assess clonal mutations in the non hematopoietic compartment. We used bone marrow mononuclear cells as germline controls. Validation was carried out with amplicon based resequencing. Alongside we provide RNA Sequencing of MDS and healthy MSCs.

  Study EGAS00001005051

• Nuclease deficiencies alter plasma cell-free DNA methylation profiles (Mouse samples)

  The dataset contains sequencing data in wildtype, Dnase1-deficient and Dnase1l3-deficient mice. We performed 2 x 75bp paired-end whole genome bisulfite sequencing of pooled plasma cell-free DNA (cfDNA) and buffy coat genomic DNA. The effects of DNASE1L3 or DNASE1 deficiency on cfDNA methylation was explored in plasma of mice deficient in these nucleases.

  Dataset EGAD00001007751

• Single-nucleus RNA-sequencing of normal adrenal cortex and adrenocortical tumors

  CellRanger counts processed with the Cell Ranger software v3.1.0.

  Dataset EGAD50000000836

• STAG2-ChIP-Seq of STAG2-mutated and cohesin-wildtype adult AMLs

  ChIP-Seq targeting the cohesin subunit STAG2 in STAG2-mutant or cohesin wildtype adult AMLs.

  Dataset EGAD00001011205

• RNAseq of blood, fat and muscle samples from 45,X, 46,XX, 46,XY and 47,XXY

  Samples of blood, muscle and fat were collected from individuals with TS (n = 33) and KS (n = 22) and from male (n = 16) and female (n = 44) controls. The RNA-seq libraries were multiplexed paired-end sequenced on an Illumina Novaseq 6000 (100 bp) and subjected to initial quality control using FastQC (BAbraham Bioinformatics). In addition to trimming of low-quality ends, adaptor removal was conducted using Trim Galore with default settings (BAbraham Bioinformatics).

  Dataset EGAD00001010052

• Transcriptomic analysis of the NA-PHER2 clinical trial

  We performed whole transcriptome RNA sequencing on serial tumour biopsies collected at baseline, Day 14, and after completion of all neoadjuvant therapy from the NA-PHER2 trial. Patients received neoadjuvant treatment with the combined regimen of trastuzumab, pertuzumab, palbociclib with or without addition of fulvestrant. Transcriptomic profiles were generated from 143 samples (Baseline n = 53, Day 14 n = 49, Surgery n = 41) corresponding to 53 of the 58 patients enrolled in NA-PHER2 trial (91.4%). RNA sequencing was performed on total RNA samples derived from formalin-fixed, paraffin-embedded (FFPE) tissue sections. RNA-Seq libraries were produced using NEBNext® Ultra™ II Directional RNA Library Prep Kit. The capture was then performed on cDNA libraries with the Twist Human Core Exome Enrichment System according to supplier recommendations (Twist Bioscience). The obtained eluted-enriched DNA samples was then sequenced on an Illumina NovaSeq as paired-end 100bp reads. FASTQ files are provided.

  Dataset EGAD50000000363

• Single cell RNA seq component of ATAC-RNA multiome analysis of a four weeks post conception embryo head

  Four single-cell RNA libraries were generated from an unbiased sample of cells of a human four weeks post conception embryo using the 10X Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC+Gene Expression kit (10X Genomics) according to the manufacturer’s protocol.

  Dataset EGAD50000001501

• Single cell ATAC seq component of ATAC-RNA multiome analysis of a four weeks post conception embryo head

  Four single-cell ATAC libraries were generated from an unbiased sample of cells of a human four weeks post conception embryo using the 10X Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC+Gene Expression kit (10X Genomics) according to the manufacturer’s protocol.

  Dataset EGAD50000001502

• Total RNA sequencing of fibroblasts from an control individual

  Total RNA sequencing of fibroblasts from an individual with 30-55x GCC repeats in the FMR1 5'UTR. Libraries were prepared with total RNA with Ribo-Zero ribosomal RNA depletion (illumina), and sequenced paired-end, 75bp on a NextSeq 550 system. This dataset contains three RNA-sequencing replicates from the same cell line.

  Dataset EGAD50000000922

• Single-cell TCR sequencing of DQ2.2-glut-L1-specific T cells

  In order to characterize the T cell receptor (TCR) repertoire of DQ2.2-glut-L1-specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-α and TCR-β genes of the single HLA-DQ2.2:DQ2.2-glut-L1 tetramer binding CD4+ T cells isolated from six T-cell lines (TCLs) of four Celiac disease patients.

  Dataset EGAD00001005047