14501 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Establishment of Human Trophoblast Stem Cells from Term Smooth Chorion

  Human trophoblast stem (TS) cells, which were established from blastocysts and first-trimester placental villi, can differentiate into the all trophoblastic subtypes, extravillous trophoblast (EVT) cells and syncytiotrophoblast (ST) cells. We newly generated human TS cells from the term smooth chorion (Ch-TS cells). They has the potential to differentiate into both ST and EVT cells as same as human TS cells derived from early placental villi. The transcriptomic profile of Ch-TS cells is also similar to conventional human TS cells.

  Study JGAS000777

• genetic analysis of carcinogenesis in GAPPS

  Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is an autosomal dominant syndrome characterized by polyposis localized in the gastric body and fundus with a strong tendency for adenocarcinoma. The genetic mutations that accumulate during the progression from normal mucosa through fundic gland polyps (FGPs) to carcinoma in GAPPS remain unclear.We investigated the evolutionary process from normal mucosa to FGPs and carcinoma in GAPPS. Through comprehensive mutational and transcriptome analyses, we aimed to provide insights into the biology of this disease.

  Study JGAS000843

• Multiregional single nuclei RNA-seq and WGS of prostate cancer

  This study investigates the clonal evolution and metastatic dissemination of prostate cancer using multiregional single-nuclei RNA sequencing (snRNA-seq) and low-pass whole-genome sequencing (WGS) data from 43 spatially distinct tumor areas in five patients with locally advanced prostate cancer, including both primary and regional lymph node samples. We employed the Chromium Next GEM Single Cell 3’ Kit (v3/3.1, 10x Genomics) for single-nuclei transcriptome profiling and constructed bulk WGS libraries using the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs) from the same pool of nuclei extracted from each area. snRNA-seq data were aligned to the human genome (GRCh38-1.2.0_premrna) using 10x Genomics Cell Ranger v5.0.0, while WGS reads were aligned to the human reference genome (GRCh38) with BWA MEM, achieving an average sequencing depth of 0.3X for low-pass WGS and 16X after resequencing.

  Dataset EGAD50000001357

• Integrated Methylation and Copy Number Analysis for Non-invasive Bladder Cancer Detection in Urine

  The molecular analysis of urine cell-free DNA (cfDNA) offers a non-invasive tool to advance bladder cancer (BC) management. Assessment of somatic copy number aberrations (SCNA) and DNA methylation, as singular or complementary analysis, have emerged as promising approaches for BC detection. Here, we developed an integrated analysis to assess both SCNA and targeted methylation changes from the same template molecules, named the iSECURE (integrated SEquencing-based Copy number and methylation analysis in URinE) method.

  Study EGAS50000001350

• Khoe-San Genome Project

  The dataset contains BAM files of whole genome sequencing data of African Khoe-San population (n=169, 30X coverage) recruited from South Africa and Namibia. The population captured the true extent of human genetic diversity as represent the earliest diverged human population. The project described a detailed divergence of human population and identified positive selections associated forager lifestyles in Khoe-San population. These findings emphasise an inclusive catalogue with better representation of the earliest human genomic diversity to better advance biomedical research.

  Study EGAS50000001408

• Comprehensive molecular profiling of pulmonary pleomorphic carcinoma

  Information regarding the molecular features of pulmonary pleomorphic carcinoma (PPC) is insufficient. Here, we performed next-generation sequencing to determine the genomic and transcriptomic profiles of PPC. Whole exome sequencing (WES) of fresh-frozen tissue samples and target-capture sequencing of formalin-fixed-paraffin-embedded (FFPE) samples were performed. Fresh-frozen tissue samples and FFPE samples were subjected to WES and target-capture sequencing as normal control, respectively. Fresh-frozen tissue samples and 56 FFPE samples were subjected to RNA-seq.

  Study JGAS000297

• The genetic analysis of circulating tumor DNA in blood of the digestive cancer patients to investigate the prognostic factors of metastasis and reccurence.

  A Darwinian evolutionary shift occurred early in the neutral evolution of advanced colorectal carcinoma (CRC) and copy number aberrations (CNA) were essential in the transition from adenoma to carcinoma. Subsequent to the primary evolution, we now focus on the evolutionary principle of the genome to foster postoperative recurrence of CRC. SO, We compared CNA, single nucleotide variance (SNV), RNA sequences between 8 primary and 11 metastatic sites from 10 CRCR cases.

  Study JGAS000221

• Identification of therapeutic target molecules for prostate cancer by using next generation sequencer

  Comprehensive transcriptional characterization of cancer tissues can reveal important molecular signatures associated with the disease progression. Long non-coding RNA (LncRNA) has a diversity of functions such as transcription, epigenetic and gene regulation in cancer cells including prostate cancer cells. Here, we performed directional RNA-sequence (RNA-seq) on clinical samples obtained from prostate cancer (PC) and lethal castration-resistant PC (CRPC) patients to identify novel molecular signatures including protein coding genes and non-coding RNAs induced in CRPC tissues.

  Study JGAS000198

• Elucidation of genomic pathology of a patient with concurrent acute myeloid leukemia and mediastinal germ cell tumor

  The occurrence of a mediastinal germ cell tumor (GCT) and hematological malignancy in the same patient is very rare. Whole exome sequencing was performed for concurrent acute myeloid leukemia (acute megakaryoblastic leukemia) and mediastinal germ cell tumor. Somatic mutations, such as TP53 or PTEN, were commonly identified in both acute myeloid leukemia and mediastinal germ cell tumor, suggesting the common founder clone. Normal buccal cells were used as a control. Illumina NextSeq 500 platform were used.

  Study JGAS000211

• Single-cell RNA sequencing of human omental tissue in benign and metastatic ovarian cancer

  To elucidate the cellular and molecular mechanisms underlying omental homeostasis and its transformation during ovarian cancer metastasis, a human omental cell atlas was generated encompassing both benign and metastatic conditions. Single-cell RNA sequencing was performed on freshly dissociated omental tissue samples from patients with newly diagnosed benign and malignant disease. Samples collected during diagnostic surgery covered distinct anatomical regions, enabling comparison between non-metastasized omentum and sites along the metastatic gradient, including distant, peritumoral, and tumor core areas.

  Study EGAS50000001465