14388 results for ""Pennsylvania+German"+ACS+study+'Socius'+open+access"

in 24.69 milliseconds.

• DDX50 Cooperates With STAU1 to Effect Stabilization of Pro-Differentiation RNAs

  This study was undertaken to determine the role of DDX50 in epidermal homeostasis. Primary neonatal foreskin keratinocytes were obtained from discarded surgical samples at a California hospital. Samples were anonymous and not selected. DDX50, which was associated with STAU1, was found to promote epidermal differentiation and transcript stability using the methods of RNA-seq, CLIP-seq and DMS-MaP-seq.

  Study phs003766

• WGS of pre-T cell receptor-alpha immunodeficiency proband and family

  In this study, we describe the role of whole genome sequencing (WGS) in providing a definitive diagnosis for a child with T cell deficiency, where targeted panel sequencing of SCID genes and whole exome sequencing had failed. A novel homozygous 8kb deletion in PTCRA, encoding pTCR, was identified. WGS sequence data from the proband, proband’s mother, and proband’s father are deposited.

  Study EGAS50000000609

• Harnessing the Electronic Health Record to Predict Risk of Cardiovascular Disease: Sangre Por Salud (SPS) Biobank GWAS Data

  These data are from subjects in the Sangre Por Salud (SPS) Biobank, a Latino population from the Southwest United States. Subjects were genotyped in 2 batches on the Illumina Multi-ethnic Global Array. Data from this study were used for testing a new cardiovascular risk score and evaluating polygenic risk scores. SPS biobank GWAS data is available on 3699 subjects.

  Study phs003553

• FluOMICS

  The FluOMICS project is to generate predictive models of influenza virus pathogenesis, leveraging previous collaborations that generated global datasets and models that predict the severity of disease caused by three influenza virus strains with different levels of virulence. This case-control study of patients diagnosed with severe and mild influenza virus disease evaluates associations between potential molecular regulators of the host response and determinants of disease outcome.

  Study phs003407

• Constrained hypermutation and absence of TERT promoter mutations in Lynch syndrome-associated urothelial cancer

  Lynch syndrome is a hereditary condition characterized by defective DNA mismatch repair and high incidence of several cancers, including urothelial cancers (UC) of the upper urinary tract and bladder. We set out to study the somatic landscape of LS-associated urothelial cancer (LS-UC) by analyzing 41 surgical tumor samples and 3 urine DNA samples from 34 LS-UC patients.

  Study EGAS50000000831

• Base modification analysis using single molecule real-time sequencing

  Based on the kinetic characteristics of single-molecule real-time sequencing, we implement a method to directly detect DNA modifications such as 5mC. However, there are room to further improve the accuracy of whole-genome-wide DNA modifications. Therefore, this study aims to utilize deep learning methods for the comprehensive profiling of multiple DNA modifications, including 5mC, 5hmC, and 6mA, using SMRT-seq.

  Study EGAS50000000366

• Human Cancer-Targeted Immunity via Transgenic Hematopoietic Stem Cell Progeny

  Analysis of a patient biopsy from the clinical trial (NCT03240861), a first-in-human study of transgenic NY-ESO-1 TCR- T cells and NY-ESO-1 TCR+ sr39tk autologous hematopoietic stem cells tandem therapy for solid tumors after myeloablative conditioning chemotherapy with busulfan and fludarabine. Single-cell RNAseq and single-cell ATACseq analysis from peripheral blood mononuclear cells obtained from subject NYSCT-03.

  Study phs003898

• Low T cell diversity is associated with poor outcome in bladder cancer - Total RNAseq data

  T cells are crucial effector cells in the endogenous defense against cancer, yet the clinical impact of their quantity, diversity, and dynamics remains underexplored. In this study we performed total RNAseq on blood samples from 8 patients with muscle invasive bladder cancer. The goal was to compare blood T cell subtype composition between patients with low and high TCR diversity.

  Study EGAS50000000939

• Longitudinal Single-cell Genomic Analysis of Initial and Recurrent Meningioma

  This study investigates the genomic evolution of meningioma through single-cell whole genome sequencing analysis of paired tumor samples. We analyzed tumor tissues from initial and recurrent meningiomas from the same patients to understand clonal evolution and tumor progression. The research aims to characterize copy number alterations and genomic heterogeneity at single-cell resolution across different time points of tumor development.

  Study EGAS50000000860

• Collagen Proteostasis in Health and Disease

  This study uses human iPSC-derived cartilage to investigate the effects of the p.Arg719Cys mutation in the COL2A1 gene, which is linked to precocious osteoarthritis. Using a CRISPR-edited isogenic cell line pair, we compared wild-type and mutant cartilage for matrix defects and cellular stress responses. We performed RNA-sequencing and quantitative proteomics to characterize changes in gene expression, protein interactions, and collagen folding.

  Study phs004112

• Evaluation of novel therapies using primary cultured gynecological cancer cells and search for predictors of efficacy

  The objective of this study is to establish an optimal method to evaluate the anti-tumor efficacy and biological activity of the novel therapies under investigation in our department using cancer tissues and cells derived from patients with gynecological malignancies in vitro and to evaluate them in practice. This research will contribute to the development of new treatments for gynecological cancer.

  Study JGAS000809

• Spatial transcriptome analysis for elucidating progression of early lung adenocarcinoma

  In this study, we performed spatial transcriptome analysis of adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) to identify molecular events which occur during progression of ealry lung adenocarcinoma. For the analysis, we used cancer tissues which were precisely classified by Noguchi classification. Using the obtained data, we elucidated key molecular changes during tumor cell progression and their associated microenvironment statuses.

  Study JGAS000677

• Single cell atlas of relapsed/refractory large B-cell lymphoma

  Relapsed/refractory large B-cell lymphomas (rrLBCL) are clinically and biologically diverse lymphoid malignancies with intricate microenvironments that play a key role in disease development. In this study, we used single-nucleus multiome profiling along with bulk DNA and RNA sequencing on 120 tumor and control biopsies to comprehensively characterize the various cell types and subsets found in rrLBCL tumors.

  Study EGAS50000001293

• Excised DNA Circles from V(D)J Recombination Promote Relapsed Leukaemia

  In this study, we show that ESCs replicate and persist through many cell generations. High ESC copies at diagnosis of BCP-ALL strongly correlate with subsequent relapse. These data provide the first demonstration that the V(D)J recombination by-product, when replicated to elevated levels, potently associates with the V(D)J recombinase to cause adverse disease outcomes.

  Study EGAS50000001043

• Excised DNA Circles from V(D)J Recombination Promote Relapsed Leukaemia

  In this study, we show that ESCs replicate and persist through many cell generations. High ESC copies at diagnosis of BCP-ALL strongly correlate with subsequent relapse. These data provide the first demonstration that the V(D)J recombination by-product, when replicated to elevated levels, potently associates with the V(D)J recombinase to cause adverse disease outcomes.

  Study EGAS50000000407

• Somatic inflammatory gene mutations accumulate in human ulcerative colitis epithelium

  We performed whole exome sequencing and targeted sequencing of ulcerative colitis with/without colitis associated neoplasm and healthy indivisuals. The aim of this study was to calculate the influence of inflammation and age on a count of genetic mutations in colonic epithelium, and to identify the specific signal pathways on which the significant genetic mutations accumulating in ulcerative colitis patients' colonic epithelium.

  Study JGAS000199

• Viral integration analysis of hepatocellular carcinoma using virus capture sequence.

  Hepatitis B viral (HBV) DNA is frequently integrated into the genome of hepatocellular carcinoma (HCC) in patients with chronic HBV infection (chronic HBV, hereafter), whereas it is yet to be clarified in patients after HBV disappearance (prior HBV, hereafter). This study aimed to identify viral integration such as HBV and adeno-associated virus type 2 (AAV2) into the HCC genome as oncogenic event.

  Study JGAS000194

• single cell RNA-seq of small cell lung cancer circulating tumor cells

  This study investigated the transcriptomic profile of circulating tumor cells from three small cell lung cancer patients. CTCs were enriched from the blood of three SCLC patients using the CTC-iChip followed by magnetic depletion of RBCs. The enriched samples were processed with the 10x Genomics Chromium platform (Chromium GEM-X Single Cell 3' Kit v4) and sequenced on a NextSeq 2000 system.

  Study EGAS50000001401

• Identification of New Therapeutic Targets for Renal Medullary Carcinoma via Integrated Genomic and Transcriptomic Profiling

  Renal medullary carcinoma (RMC) is a rare, aggressive kidney cancer associated with sickle cell trait, characterized by SMARCB1 loss and resistance to conventional therapies used for other renal cell carcinomas (RCC). We conducted whole exome sequencing (WES) on RMC samples. This study provides a large molecular characterization of RMC, highlighting TROP2 and other cell surface markers as promising therapeutic targets.

  Study EGAS50000001280

• Whole-exome sequencing and RNA-seq data of paired normal-tumour samples from MMR-proficient early-onset colorectal cancer patients

  This study aims to identify novel hereditary colorectal cancer predisposition genes by performing whole-exome sequencing and RNA-seq of paired normal colonic mucosa and colorectal cancer samples from 19 patients diagnosed with MMR-proficient colorectal cancer at an age of 50 years or younger. Both whole-exome and RNA sequencing were performed on the Illumina platform.

  Study EGAS50000001296

• RNA-seq of STIC lesions and adjacent normal samples

  In this study, we characterize premalignant lesions of the fallopian tube (serous tubal intraepithelial carcinomas) to explore the earliest events of tumorigenesis following mutation of the TP53 tumor suppressor gene. We conduct laser capture microdissection to isolate premalignant cells from adjacent normal cells, and subject isolated tissues to RNA-seq. Our findings reveal the earliest transcriptional changes established during premalignancy within the fallopian tube.

  Study EGAS50000000200

• EXPRESSION OF ANTIBODY-DRUG CONJUGATE TARGETS IN BREAST CANCER METASTASES AND NORMAL TISSUE

  Using bulk mRNA sequencing, we investigated the expression of 72 ADC targets, which are clinically approved or under investigation, in 909 samples (64 primary untreated, 749 metastatic, 96 normal) from 30 female patients from our post-mortem tissue donation program UPTIDER (NCT04531696). The study explores changes in target expression across multiple samples to identify novel targets of clinical interest and validation

  Study EGAS50000001334

• Indigenous American Diversity and Evolution

  The Indigenous American Genomic Diversity Project (IAGDP) investigates the genomic diversity and evolutionary history of Native American populations, which remain underrepresented in global genomic research. As part of this effort, we generated high-coverage whole-genome sequences individuals sampled across eight Latin American countries. This study provides a resource for investigating population structure, demographic history, and adaptive evolution in Indigenous American populations.

  Study EGAS50000001664

• HipSci___Whole_Exome_sequencing___Congenital_hyperinsulinia

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with congenital hyperinsulinia

  Study EGAS00001001977

• HipSci___Whole_Exome_sequencing___Kabuki

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Kabuki syndrome

  Study EGAS00001001981

• HipSci HumanExome BeadChip analysis - Hereditary Cerebellar Ataxias

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Cerebellar Ataxias.

  Study EGAS00001002005

• HipSci HumanExome BeadChip analysis - monogenic diabetes

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with monogenic diabetes.

  Study EGAS00001001273

• HipSci___Whole_Exome_sequencing___Cardiomyopathy

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with hypertrophic cardiomyopathy

  Study EGAS00001001980

• HipSci HumanExome BeadChip analysis - Kabuki syndrome

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Kabuki syndrome.

  Study EGAS00001002007

• HipSci HumanExome BeadChip analysis - Macular Dystrophy

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Macular Dystrophy.

  Study EGAS00001002014

• HipSci___Whole_Exome_sequencing___Alport

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Alport syndrome

  Study EGAS00001001974

• HipSci HumanHT 12 Expression BeadChip analysis - Retinitis Pigmentosa

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Retinitis Pigmentosa.

  Study EGAS00001002030

• Genetic_screening__of_GPI_anchor_protein_synthesis__

  This study will analyse the guide sequence which were used for making mutations in the Cas9-expressing cells. We used GeCKO v2 library which were released by Feng Zhang, 2014. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001256

• Whole genome landscape of 25 metastatic cutaneous squamous cell carcinoma cSCC patients

  whole genome sequencing on lymph node metastases and blood DNA from 25 cSCC patients with regional metastases of the head and neck. We designed a multifaceted computational analysis at the whole genome level to provide a more comprehensive perspective of the genomic landscape of metastatic cSCC. This study contains the majority of 15 samples which are previously submitted in EGAC00001001100.

  Study EGAS00001006378

• HipSci___Whole_Exome_sequencing___Retinitis_Pigmentosa

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Retinitis Pigmentosa

  Study EGAS00001001984

• Diverse modes of genomic alterations in hepatocellular carcinoma

  Hepatocellular carcinoma is the most prevalent type of liver cancer. We intended to study the genomic landscape of this disease. We conducted whole-genome, exome and transcriptome sequencing for 42 patients. We show diverse modes in which the HCC genome is affected in these patients, including well-known and novel mutations, structural variations, and Hepatitis B-virus integration into the genome.

  Study EGAS00001000824

• ARGO_GWAS

  Osteoarthritis (OA) is the most common form of arthritis affecting ~40% of people over the age of 70. OA is characterised by cartilage degeneration in the synovial joints and presents one of the leading causes of chronic disability and impaired quality of life in the developed world.The ARGO study is an ongoing collection of well-phenotyped OA patients undergoing total joint replacement and is based in Greece.

  Study EGAS00001000917

• HipSci Illumina 450K Methylation analysis-Rare_BBS

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Methylation analysis using the Infinium HumanMethylation450 BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Bardet-Biedl syndrome.

  Study EGAS00001001274

• Whole_Genome_sequencing_of_individuals_from_Carlantino__Italy

  This study includes whole-genome sequencing data (at 4x depth) of 100 individuals from an Italian genetic isolate population (Carlantino, abbreviated CARL) of the Italian Network of Genetic Isolates (INGI). The INGI-CARL_SEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits.

  Study EGAS00001000460

• Developing somatic copy number and mutation calling tools for a bespoke sequencing platform

  We previously developed a linked-read sequencing platform (DigiPico) for analysing whole cancer genomes from picogram quantities of tumour DNA. The aim of this study was to develop and evaluate the specialised computational approaches required to obtain clinically useful results from the raw data. To this end, we performed matched DigiPico, bulk tumour and germline WGS on samples from four patients.

  Study EGAS00001007195

• HipSci___Whole_Exome_sequencing___Bardet_Biedl_Syndrome

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Bardet-Biedl syndrome

  Study EGAS00001000969

• HipSci___Whole_Exome_sequencing___BPD

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with blood and platelet disorders

  Study EGAS00001001976

• HipSci___Whole_Exome_sequencing___Ataxia

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with hereditary cerebral ataxia

  Study EGAS00001001978

• HipSci HumanExome BeadChip analysis - Alport Syndrome

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Alport Syndrome.

  Study EGAS00001002009

• HipSci HumanExome BeadChip analysis - Retinitis Pigmentosa

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Retinitis Pigmentosa.

  Study EGAS00001002015

• HipSci HumanHT 12 Expression BeadChip analysis - Kabuki syndrome

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Kabuki syndrome.

  Study EGAS00001002022

• HipSci HumanHT 12 Expression BeadChip analysis - Congenital Hyperinsulinia

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Congenital Hyperinsulinia.

  Study EGAS00001002025

• HipSci Illumina 450K Methylation analysis - monogenic diabetes

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Methylation analysis using the Infinium HumanMethylation450 BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with monogenic diabetes.

  Study EGAS00001001275

• HipSci___Whole_Exome_sequencing___Monogenic_Diabetes

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Monogenic Diabetes.

  Study EGAS00001001140

• Transcriptomes_of_human_lymphocytes

  In this study we will compare the single cell transcriptomes of immune cells from asthmatics responding to steroids, those refractory to steroids, and a control population.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001755