15016 results for "cancer studies using rna-seq"

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• Structure and Diversity of Urinary Cell-Free DNA Informative of Host-Pathogen Interactions in Human Urinary Tract Infection

  The risk of acquiring urinary tract infection (UTI) is very high for patients who have received kidney transplants; nearly half will develop bacteriuria and an eighth viruria via BK polyomavirus in the first three years following transplantation. Current methodology for diagnosing viral and bacterial infections, while well practiced, is often limited in scope. The advent of next generation sequencing of cell-free DNA has shown promise in its ability to capture multiple perspectives of human health from discovering the origin of cell-free DNA in plasma; such a diagnostic has not been readily applied to urinary cell-free DNA. In this study, we selected 141 urine samples from a cohort of kidney transplant patients, which were collected and stored at Weill Cornell Medical College - New York Presbyterian Hospital. Of these samples, 43 samples were determined to be culture positive (> 10,000 CFU) for one or more bacterial species, including E. coli, Enterococcus, Klebsiella, Haemophilus, and Raoultella. A separate 23 samples were confirmed for BK virus nephropathy, with presence of BK polyomavirus confirmed via qPCR. We also included 29 samples from 14 patients who did not develop UTIs in the first three months following transplantation, and 11 samples that were negative for BK virus nephropathy. For a full description of samples, please see the Supplementary Data 1 in https://pubmed.ncbi.nlm.nih.gov/29925834/. From these urine samples, we aimed to capture and sequence urinary cell-free DNA using a single-stranded library preparation. In addition, we performed whole-genome bisulfite sequencing to 170 plasma samples collected from 27 hematopoietic cell transplant patients who developed graft-versus host disease and BK polyomavirus infection. We also performed Sample-Intrinsic microbial DNA Found by Tagging and sequencing (SIFT-seq) on 196 cell-free DNA (cfDNA) samples (154 plasma and 42 urine) collected from five groups of subjects. For a full description of samples, please see publications in PMID: 35864089 and PMID: 35058359.

  Study phs001564

• Colorectal_organoids_and_tumoroids___pulldown

  Targeted capture of cancer gene panel bait set in single cell derived organoids from colon tissue and colorectal cancer from 1 patient.

  Study EGAS00001000869

• DEMENTIA-SEQ: WGS in Lewy Body Dementia and Frontotemporal Dementia

  Lewy body dementia, amyotrophic lateral sclerosis/frontotemporal dementia, and multiple system atrophy are age-related, neurodegenerative syndromes that are poorly understood. Delineating the genetic risk that is driving the pathophysiology of these neurological diseases is fundamental for understanding disease mechanisms and for developing disease-modifying treatments. In version 1 of the study/dbGaP deposition, we performed a whole-genome sequencing study consisting of 7,403 total samples, including 2,633 genomes from patients with Lewy body dementia, 2,641 frontotemporal dementia patients, and 1,980 neurologically healthy controls. Of these, 6,907 were uploaded to dbGaP as the basis of the DementiaSeq, phs001963 dataset. The data relating to these samples are available on dbGaP. In version 2 of this study/dbGaP deposition, we made much of these data available on Anvil. More specifically, data for 6,254 of these samples were also uploaded to the ALS Compute platform on AnVIL. The data for the remaining 653 samples are only available on dbGaP. The dbGaP/AnVIL Table lists the availability of dbGaP and AnVIL for each individual sample: phd008475.In version 3 of the study/dbGaP deposition, we added whole-genome sequence data generated using DNA samples obtained from 683 patients diagnosed with multiple system atrophy.

  Study phs001963

• RNA isoform repertoire of neuropsychiatric risk genes in human brain

  Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds of genomic variants that alter the expression and/or products (isoforms) made by risk genes. However, how these genes contribute to disease risk and onset through altered expression and RNA splicing is not well understood. Here we show our current understanding of gene isoforms is far from complete and reveal the precise splicing profiles of neuropsychiatric disorder risk genes. Combining our new bioinformatic pipeline IsoLamp with nanopore long-read amplicon sequencing, we deeply profiled the RNA isoform repertoire of 31 high-confidence neuropsychiatric disorder risk genes in human brain. We show most risk genes are more complex than previously reported, identifying 443 novel isoforms and 28 novel exons, including isoforms which alter protein domains, and genes such as ATG13 and GATAD2A where most expression was from previously undiscovered isoforms. The greatest isoform diversity was present in the schizophrenia risk gene ITIH4. Mass spectrometry of brain protein isolates confirmed translation of a novel exon skipping event in ITIH4, suggesting a new regulatory mechanism for this gene in brain. Our results emphasize the widespread presence of previously undetected RNA and protein isoforms in brain and provide an effective approach to address this knowledge gap. Uncovering the isoform repertoire of neuropsychiatric risk genes will underpin future analyses of the functional impact these isoforms have on neuropsychiatric disorders, enabling the translation of genomic findings into a pathophysiological understanding of disease.

  Study EGAS00001007744

• EGAD00010000574

  Pleuropulmonary blastoma samples using 250K

  Dataset EGAD00010000574

• Methylation_CASES

  CASE_SAMPLES using platform …..

  Dataset EGAD00010002368

• Methylation_CONTROLS

  CONTROL_SAMPLES using platform …..

  Dataset EGAD00010002367

• Hydroxyurea to Prevent Organ Damage in Children with Sickle Cell Anemia (BABY HUG) Phase III Clinical Trial and Follow-Up Observational Studies I and II

  Sickle cell anemia is associated with substantial morbidity from acute complications and organ dysfunction beginning in the first year of life. In 1995, the Multicenter Study of Hydroxyurea (MSH) (dbGaP phs002348) demonstrated that, in adults, hydroxyurea is effective in decreasing the frequency of painful crises, hospitalizations for crises, acute chest syndrome, and blood transfusions by 50%. The phase I/II study of hydroxyurea in children (HUG KIDS) demonstrated that children have a response to hydroxyurea similar to that seen in adults in terms of increasing fetal hemoglobin levels and total hemoglobin, and decreasing complications associated with sickle cell anemia. In addition, this study demonstrated that the drug does not adversely affect growth and development between the ages of 5 and 15. A pilot study of hydroxyurea (HUSOFT) given to children between the ages of 6 months and 24 months demonstrated that the drug was well tolerated and that the fetal hemoglobin levels rose and remained elevated compared to baseline with continued hydroxyurea administration. A Special Emphasis Panel (SEP) met on April 12, 1996 to review the results of the MSH trial and the progress to date of the HUG KIDS study. The SEP recommended that NHLBI undertake the BABY HUG trial. The BABY HUG Randomized Controlled Trial concluded that hydroxyurea treatment in very young children seemed to have an acceptable safety profile and to reduce complications of sickle cell anemia. However, more data were needed on the long-term safety of hydroxyurea use in very young children. As a result, follow-up studies were initiated. The Follow-Up Study II provided longer follow-up than Follow-Up Study I, and included more assessment types than Follow-Up Study I.The BABY HUG program consisted of three related studies, each of which has associated datasets and bio-specimens. A randomized controlled trial comparing hydroxyurea to placebo in very young children with sickle cell anemia (BABY HUG Randomized Controlled Trial) The first observational follow-up study of children from the randomized controlled trial (BABY HUG Follow-Up Study I). All children in Follow-Up Study I were offered the option of taking open-label hydroxyurea, with treatment decisions made by the family and the clinical team caring for the child. The second observational follow-up study of children from BABY HUG Follow-Up Study I. All children in Follow-Up Study II were offered the option of taking open-label hydroxyurea, with treatment decisions made by the family and the clinical team caring for the child.The purpose of the Randomized Controlled Trial was to determine if hydroxyurea can safely prevent early end organ damage in very young children with sickle cell anemia. The purpose of the BABY HUG Follow-up Study I was to provide structured follow-up of the children enrolled in the BABY HUG Randomized Controlled Trial, in order to characterize the long-term toxicities and unexpected risks (if any) associated with treatment with hydroxyurea at an early age. The objective of Follow-Up Study II was to obtain additional data about the long-term safety and efficacy of hydroxyurea use in children with Sickle Cell Anemia through at least the first decade of life.Instructions for requesting individual-level data are available on BioData Catalyst at https://biodatacatalyst.nhlbi.nih.gov/resources/data/. Apply for data access in dbGaP. Upon approval, users may begin accessing requested data in BioData Catalyst. For questions about availability, you may contact the BioData Catalyst team at https://biodatacatalyst.nhlbi.nih.gov/contact.

  Study phs002415

• H3K27ac HiChIP Dataset for 19 T-ALL patients and one normal control sample

  19 H3K27ac HICHIP from T-ALL patient samples and one healthy normal control sample. Reads were aligned to HG38 reference.

  Dataset EGAD50000000023

• scRNA-seq analysis of HGSC tumors, including immune TME, before and after NACT

  Gene expression profiles of single cells from 26 tumor and ascites samples samples from 17 patients

  Dataset EGAD50000000862

• Bulk exome sequencing of primary GBM - SF 10360

  We performed bulk exome-seq on a primary GBM and a blood sample from SF10360

  Dataset EGAD00001002274

• NiCOL Study Target-seq dataset

  10 samples sequenced in Target-sequencing of a panel of 571 genes (Illumina NovaSeq 6000) - Raw FASTQ data - Annotated VCF

  Dataset EGAD00001010911

• Paired-end Whole Exome-seq analysis of the 3D spatially mapped GBM samples.

  Dataset contains 50 paired-end Whole Exome sequencing samples from 3 patients. 3 normal blood samples are also included.

  Dataset EGAD00001010289

• ChIPseq of neuroblastoma

  This dataset contains 4 samples (2x input and 2x H3K27ac ChIPseq) in the IC-pPDXC-63 cell line.

  Dataset EGAD00001006557

• ChIP sequencing from a collection of PFA tumors

  ChIP data from PFA (n = 10). Raw data provided as FASTQ. Data generated on Illumina NovaSeq 6000 PE50.

  Dataset EGAD00001009045

• H3K27ac ChIPseq of cohesin-mutated and wildtype adult AMLs

  ChIP-seq targeting the H3K27ac histone modification in cohesin-mutated (STAG2 or RAD21 mutation) and cohesin wildtype (CTRL-AMLs) AMLs.

  Dataset EGAD00001011204

• Molecular Features of Hepatocellular Carcinoma Associated with 18F-Fluorocholine PET/CT Imaging Phenotype

  Molecular imaging with 18F-fluorocholine PET/CT reveals two distinct imaging phenotypes for hepatocellular carcinoma (HCC) as a potential source of non-invasive insight into its molecular heterogeneity. Using gene set enrichment analyses, we found 18F-fluorocholine-avid tumors to be significantly enriched by genes comprising a subset of previously published HCC-related gene signatures. Significant gene sets included those from existing molecular classification systems for HCC as well as gene signatures predictive of clinical outcomes after tumor resection. PET/CT imaging using 18F-fluorocholine might therefore provide surrogate information about tumor molecular characteristics and prognosis in HCC.

  Study phs001784

• Single-Cell Transcriptomics of Adult Recurrent Respiratory Papillomatosis

  These single-cell sequencing data were generated from diseased respiratory tract papilloma tissue caused by chronic infection with HPV 6 or 11. Patients from which this tissue was derived participated in a phase I clinical trial using a novel therapeutic vaccine, but these samples were acquired before this experimental treatment. The aim of performing this single-cell sequencing study was to characterize the papilloma cells and other cells in the papilloma microenvironment with single-cell analyses using the 10X Genomics platform. The single-cell gene expression raw data files for each sample will be available in this submission.

  Study phs003349

• Comparison of transcriptomics profile of stem cell-derived beta cells from HUES8 and RC9

  Stem cell-derived islet cells have a potential to be used to restore endogenous insulin production in people with diabetes. The goal of this experiment is to compare the transcriptomics profile of stem-cell derived beta cells from two different cell lines: HUES8 (non-clinical grade) and RC9 (clinical grade) in terms of beta cell identity and maturity. Stem cell-derived islets were produced using differentiation protocol detailed in Rajaei et al. 2025 (manuscript approved in Science Translational Medicine, pending pubmed ID). Single cell transcriptomics data were generated using 10x Genomics 3' Single Cell Gene Expression kit.

  Study EGAS50000000905