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• Mutational analysis of an oligoprogressive sarcomatoid hepatocellular carcinoma treated with an immune checkpoint inhibitor.

  In this study, we describe a patient diagnosed with metastatic sarcomatoid hepatocellular carcinoma that showed a remarkable tumor response to Nivolumab, an immune checkpoint inhibitor, followed by an oligoprogression. Molecular analysis of the primary tumor in addition to a bone and brain metastasis was performed and we were able to identify driver genetic alterations indicating a possible role in the tumorigenesis process besides some alterations that may be associated with metastasis.

  Study EGAS00001005064

• Nuclease deficiencies alter plasma cell-free DNA methylationprofiles (Human)

  The effects of DNASE1L3 or DNASE1 deficiency on cfDNA methylation was explored in plasma of mice deficient in these nucleases and in DNASE1L3-deficient humans. Compared to wildtype cfDNA, cfDNA in Dnase1l3-deficient mice was significantly hypomethylated, while cfDNA in Dnase1-deficient mice was hypermethylated. The cfDNA hypomethylation in Dnase1l3-deficient mice was due to increased fragmentation and representation from open chromatin regions (OCRs) and CpG islands (CGIs). These findings were absent in Dnase1-deficient mice.

  Study EGAS00001004897

• Olink Explore Protein Expression

  Serum samples (DC, CRSsNP, CRSwNP, N-ERD, n=20 each) were subjected to the Olink Explore 3072 analysis including the following panels: Olink Explore 384 Cardiometabolic and Cardiometabolic II, Olink Explore 384 Inflammation and Inflammation II, Olink Explore 384 Neurology and Neurology II, Olink Explore Oncology and Oncology II. The latter had 4 failed samples. From the originally 2925 unique proteins determined, 84 proteins had missing values in all samples and were removed. Further 164 proteins had >50% of values below LOD across all four groups and were removed with remaining values below threshold adjusted to LOD. This data cleaning left 2695 unique assays (2677 unique proteins) in serum to be analysed. Additionally, six assays (LMOD1, IDO1, SCRIB, CXCL8, IL6, TNF) were measured four times each in different panel.

  Dataset EGAD50000001327

• Total RNA sequencing of 32 chronic lymphocytic leukemia (CLL) patients

  Peripheral blood mononuclear cells (PBMC) of CLL patients were isolated by density-gradient centrifugation over Linfosep (Biomedics, Madrid, Spain). B cells were purified with a CD19+ magnetic-bead system (MidiMACS, Miltenyi Biotec, Bergish Gladbash, Germany) according to the manufacturers’ instructions. Mean B-cell purity was >99% and the mean percentage of CD5+/CD19+ cells after purification was >98%, as measured by flow cytometry. Total RNA was extracted from purified cells in a single step using TriPure Isolation Reagent (Roche Applied Science, Vilvoorde, Belgium).Whole transcriptome sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina). Libraries underwent 2 × 76 bp paired-end sequencing on a HiSeq 2500 instrument (Illumina). The median number of paired-end reads was 60.5 million (range, 49.7-79.7 million).

  Dataset EGAD00001004047

• Inter and intra - tumor heterogeneity in Colorectal Cancer

  We used high depth massive parallel sequencing analyses to study 27 CRC (colorectal cancer) patients, with a total of 97 tumors (both primary and matched metastases) in addition to healthy control samples. We found inter-tumor concordance for coding mutations; in contrast, gene copy numbers were found to be highly discordant between primary tumors and metastases as validated by fluorescent in-situ hybridization. in a further step, we dissected a single tumor into 68 spatially defined samples and sequenced them separately. Here we identify evenly distributed coding mutations in APC and TP53 in all tumor areas, yet highly variable gene copy numbers in numerous genes.

  Study EGAS00001002150

• Gene expression profiling by RNAseq of multiple cell types derived from patients with LSD1 mutations and healthy controls, and in isogenic cell lines with LSD1 mutation introduced by CRISPR-Cas9

  Cell lines (fibroblasts, reprogrammed from them hiPSCs and differentiated from hiPSCs endoderm, mesoderm and neuronal cells) derived from two male CPRF patients carrying distinct LSD1 mtuations and their healthy fathers as controls were subjected to gene expression analysis by bulk RNAseq to identify mis-regulated genes. Some cell lines were subject to treatment with HDAC inhibitor valproic acid (VPA) or DMSO as controls and also underwent RNAseq analysis. Two isogenic LSD1 mutant hiPSC lines with CRISPR-edited Family B LSD1 mutation were also used for RNAseq analysis (after endoderm differentiation, with or without VPA treatment).

  Study EGAS00001008240

• Single Cell Genome Sequence for DLP+ library A96141A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA604 passage 8 on DLP+ library A96141A

  Dataset EGAD00001009513

• A98256A

  Whole genome sequencing for single cells for library A98256A 1372 cells; filetype=bam

  Dataset EGAD00001007124

• A98172A

  Whole genome sequencing for single cells for library A98172A 898 cells; filetype=bam

  Dataset EGAD00001007123

• A96240A

  Whole genome sequencing for single cells for library A96240A 1493 cells; filetype=bam

  Dataset EGAD00001007121

• A96225C

  Whole genome sequencing for single cells for library A96225C 1034 cells; filetype=bam

  Dataset EGAD00001007120

• A96225B

  Whole genome sequencing for single cells for library A96225B 959 cells; filetype=bam

  Dataset EGAD00001007119

• A96181C

  Whole genome sequencing for single cells for library A96181C 1216 cells; filetype=bam

  Dataset EGAD00001007117

• A96178B

  Whole genome sequencing for single cells for library A96178B 846 cells; filetype=bam

  Dataset EGAD00001007116

• A96130B

  Whole genome sequencing for single cells for library A96130B 1267 cells; filetype=bam

  Dataset EGAD00001007114

• A96118A

  Whole genome sequencing for single cells for library A96118A 1193 cells; filetype=bam

  Dataset EGAD00001007113

• A96115B

  Whole genome sequencing for single cells for library A96115B 1201 cells; filetype=bam

  Dataset EGAD00001007112

• A96115A

  Whole genome sequencing for single cells for library A96115A 1635 cells; filetype=bam

  Dataset EGAD00001007111

• A95731B

  Whole genome sequencing for single cells for library A95731B 1307 cells; filetype=bam

  Dataset EGAD00001007110

• A95675A

  Whole genome sequencing for single cells for library A95675A 668 cells; filetype=bam

  Dataset EGAD00001007109

• A95663B

  Whole genome sequencing for single cells for library A95663B 1364 cells; filetype=bam

  Dataset EGAD00001007108

• A95653B

  Whole genome sequencing for single cells for library A95653B 1342 cells; filetype=bam

  Dataset EGAD00001007107

• A95646A

  Whole genome sequencing for single cells for library A95646A 1071 cells; filetype=bam

  Dataset EGAD00001007106

• A95634B

  Whole genome sequencing for single cells for library A95634B 1335 cells; filetype=bam

  Dataset EGAD00001007105

• A95626A

  Whole genome sequencing for single cells for library A95626A 1040 cells; filetype=bam

  Dataset EGAD00001007103