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• BASIS_RNAseq

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000707

• Breast_Cancer_FRT_RNA_seq

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000420

• Balanced_Ependymoma

  We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Study EGAS00001000174

• (h)MeDIP-Seq of high-risk prostate cancer

  Immunoprecipitation of methylated and hydroxymethylated DNA was performed on DNA isolated from tumoral and non-tumoral prostate tissue of patients with high-risk disease. Samples were sequenced on the Illumina HiSeq as 50 bp single end.

  Study EGAS00001001019

• Breast_Cancer_Whole_Genome_Sequencing

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000210

• Triple_Negative_Breast_Cancer_RNA_Sequencing

  We propose to definitively characterise the somatic genetics of triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000377

• Blueprint RNAseq profile of purified plasma cells from multiple myeloma patients and tonsils of healthy donors

  In the context of an epigenomic study of multiple myeloma, a have generated RNAseq profiles of purified plasma cells from 11 multiple myeloma patients and tonsils of 4 healthy donors

  Study EGAS00001001110

• BCL11B enhancer hijacking defines a subtype of lineage ambiguous stem cell leukemia

  Hijacking of primitive hematopoietic enhancers, or generation of a neo-enhancer by genomic amplification, results in deregulation of BCL11B as the defining feature of a subset of T/myeloid leukemia

  Study EGAS00001004810

• GWAS in bullous pemphigoid in Germans

  Genome-wide association study of bullous pemphigoid in Germans, using 446 BP patients and 433 age- and sex- matched controls. 6 SNPs in the HLA locus were found to be of genome-wide significance.

  Study EGAS00001004627

• RNA Sequencing of Colorectal Liver Metastases

  Reverse-stranded paired-end 75 base-pair RNA sequencing libraries of 93 metastatic FFPE samples were constructed using Illumina Total RNA Stranded Kits. Ribosomal RNAs (rRNAs) were depleted by using the Ribo-Zero rRNA Removal Kit (Illumina). Libraries were sequenced on a HiSEQ2500 machine. Five samples were re-sequenced using paired-end 50 base-pair libraries due to the smaller insert sizes.

  Dataset EGAD00001004111

• Deciphering RBP - alternative splicing networks in ALS iPSC-MN: TDP-43, NOVA1, NOVA2 and RBFOX2 eCLIP-seq

  We produced enhanced cross-linking immunoprecipitation (eCLIP) sequencing data of the RNA binding proteins (RBP) TDP-43, NOVA1, NOVA2 and RBFOX2 in iPSC motor neurons of two healthy control individuals, respectively.

  Study EGAS00001005880

• TB-DAR Genotyping Study

  Active TB patients (sputum smear-positive and GeneXpert-positive) recruited at the Temeke District Hospital in Dar es Salaam, Tanzania, as part of a prospective study that ran between November 2013 and June 2022 (TB-DAR cohort).

  Study EGAS00001007216

• Molecular programs of melanoma brain metastases (MBM)

  We performed paired-end whole transcriptome sequencing of fresh frozen or intraoperative brain metastases of therapeutically treated stage IV melanoma patients. In addition, we analysed the epigenetic landscape of tumors usind Illumina 850k bead chip technology.

  Study EGAS00001005976

• Genomic Rearrangements in Pediatric Cancer

  This study contains a collection of samples used to determine the role and impact of genomic rearrangements in a pan cancer pediatric cohort.

  Study EGAS00001005312

• Paired-WGS-two-families-with-GBA-variants-and-Parkinsons-disease

  We performed whole- genome sequencing, rare variant filtering, segregation analysis and functional validation of PD cosegregating rare genetic variation in two families (6 samples) segregating PD associated GBA variants c.115+1G>A (ClinVar ID: 93445, ) and p.L444P (ClinVar ID: 4288) respectively. The paired WGS sequencing was run on HiSeq X Ten and the library preparation kit was Illumina TruSeq DNA nano.

  Dataset EGAD00001006561

• RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  Dataset EGAD00001001944

• Single nucleus RNA sequencing of isolated NK cells and CD56+ T cells from digested NSCLC tumor lesions

  In order to explore the intratumoral NK cell heterogeneity at a transcriptomic level, we performed matched single nucleus RNA sequencing of isolated CD45+CD3+CD56+ immune cells from 11 NSCLC patients.

  Study EGAS50000001189

• Single nucleus ATAC sequencing of isolated NK cells and CD56+ T cells from digested NSCLC tumor lesions

  In order to explore the intratumoral NK cell heterogeneity at an epigenetic level, we performed matched single nucleus ATAC sequencing of isolated CD45+CD3+CD56+ immune cells from 11 NSCLC patients.

  Study EGAS50000001190

• Whole-exome sequencing of P2RY8-CRLF2-positive ALL on Illumina HiSeq 2000, 100 bp paired-end

  Genomic DNA from leukemic and remission bone marrow mononuclear cells was isolated with the QIAamp DNA Blood Extraction Kit (Qiagen, Venlo, The Netherlands). Libraries were prepared using Nextera Rapid Capture Exome Kit (Illumina, San Diego, USA). Paired-end sequencing of 100 bp reads was performed on a HiSeq 2000 (Illumina) to obtain at least a 50 x coverage.

  Dataset EGAD00001002666

• Single-cell RNA and TCR sequencing of CSF cells and PBMCs from individuals with neurological disorders

  We performed single-cell RNA sequencing combined with T-cell receptor sequencing to characterize immune cells from cerebrospinal fluid (CSF) and peripheral blood mononuclear cells (PBMCs) of patients with multiple sclerosis and individuals with other inflammatory neurological diseases used as controls. The aim of this study was to identify and characterize T cells with TCRs shared among people with MS and enriched in the CSF compartment.

  Dac EGAC50000001015

• A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart

  Dataset includes 2 scRNA-seq samples from a 6.5-7 post-conception weeks human embryonic heart and 19 samples from 4.5-9 post-conception weeks human embryonic hearts analyzed with the Spatial Transcriptomics method. H&E stains can be sent if requested.

  Dataset EGAD00001005468

• Failure of Differentiation of the Rhombic Lip Constitutes Medulloblastoma

  We used single-cell transcriptomics to study cells from the developing human cerebellum, and show that different molecular subgroups of medulloblastoma resemble distinct glutamatergic progenitors.

  Dataset EGAD00001008381

• Bulk RNAseq data of scrambled and siRNA-mediated knock-down of the minor spliceosome snRNA U6atac

  Bulk RNAseq data of scrambled and siRNA-mediated knock-down of the minor spliceosome snRNA U6atac in androgen-sensitive LNCaP cells (L), androgen-insensitive C4-2 (C) and 22Rv1 (R) cells and in patient derived neuroendocrine organoids PM154 (P).

  Dataset EGAD00001008034

• WES data of central nervous system neoplasm patients

  Dataset containing 2068 WES tumor and control samples of central nervous system neoplasm patients. The data was sequenced on a Illumina NextSeq 500 using a NPHD2015A kit. The sequencing was always paired.

  Dataset EGAD00001009855

• Exome sequencing data from two small cell prostate cancer patients

  Exome sequencing data from two small cell prostate cancer patients - 4 cancer samples (FFPE) from Patient 1 collected at 3 different time points and 2 cancer samples (FFPE) from Patient 2 collected at 1 time point. Exonic DNA was enriched using the TruSeq Exome Kit (Illumina) and sequenced on the Illumina NextSeq 500 as 75bp paired end reads (total read length 150bp).

  Dataset EGAD00001011149