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• Molecular profiling of MBD4-deficient acute myeloid leukaemia

  We describe two cases of MBD4-deficient acute myeloid leukaemia (AML). Clinical samples were used for molecular analysis, including genomic profiling (genome and exomes), methylation analysis (RRBS) and transcriptional profiling (RNA-sequencing). An analysis and methodological description has been published: “MBD4 guards against methylation damage and germline deficiency predisposes to clonal hematopoiesis and early-onset AML” [PMID: 30049810]

  Study EGAS00001002581

• Transcriptome sequencing of myelodysplasia

  Transcriptome sequencing was performed on 214 patients with myelodysplasia in this study. RNA was obtained from bone marrow CD34+ cells (n=100) and/or bone marrow mononuclear cells (n=165). Transcriptome sequencing was performed for both cell fractions in 51 patients. We also studied bone marrow CD34+ cells and bone marrow mononuclear cells obtained from three healthy adults each.

  Study EGAS00001002346

• RNA data for MMML (EGAS00001002422)

  RNA sequencing data for MMML (3 tumor samples and 1 gcbcell)

  Dataset EGAD00001003285

• WGS data for MMML (EGAS00001002422)

  Whole genome sequencing data for MMML (7 tumors and 8 controls)

  Dataset EGAD00001003286

• RNA-Seq data for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"

  RNA-Seq data for the paper titled "Orthotopic Patient-Derived Xenografts of Pediatric Solid Tumors"

  Dataset EGAD00001003433

• Sequencing data for oesophageal and related samples - Alex Frankell et al (WGS)

  Data supporting: "The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic." Frankell et al. WGS (BAM files) 379 matched tumour-normal pairs

  Dataset EGAD00001004417

• Transcriptomic analysis of TFEB overexpression in LT-HSC, ST-HSC and MEP

  Long-term hematopoietic stem cells (LT-HSC), Short-term hematopietic stem cells (ST-HSC) and Megakaryocyte-erythrocyte progenitors (MEP) were sorted from human cord blood and cultured overnight before transduction with lentivirus to overexpress GP91 (CTRL) or TFEB. Three (LT-HSC ans ST-HSC) or six (MEP) days later, BFP+ transduced cells were sorted for RNA extraction and sequencing.

  Study EGAS00001004969

• RNA-seq following TBL1XR1 KD in human CD34+CD38- cord blood cells

  We performed RNA-seq on CD34+CD38- human cord blood (CB) cells transduced with sh_Control or sh_TBL1XR1 lentiviruses to identify differentially expressed genes. Sorted CD34+CD38- cells from 3 independent cord blood pools were transduced with lentiviruses containing BFP reporter gene. BFP+ cells were sorted 3 days post-transduction and RNA was harvested for library preparation and sequencing.

  Study EGAS00001005869

• Finding structural variation and functional consequences from the primary leukemia cells (CLL) at the single-cell level

  In this study, we aimed to identify somatic structural variation of chronic lymphocytic leukemia (CLL) at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from 63-year-old female patient.

  Study EGAS00001004925

• Genomic and epigenomic study of Japanese renal cell carcinoma including WGS, RNA-seq, ATAC-seq, and methyl-seq

  We performed whole-genomic and transcriptomic sequencing of more than 100 Japanese renal cell carcinoma (RCC) cases, including clear cell RCC, papillary RCC, chromophobe RCC, and TFE3-translocated RCC. In addition, we conducted epigenome sequencing analyses: the assay for transposase-accessible chromatin sequencing (ATAC-seq) and enzymatic methyl sequencing.

  Study EGAS00001006919