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Results Found: 7
  • Internal Dataset

    Transcriptomic profiles of mycobacteriophage D29, L5 and StarStuff

    Authors
    • Hatfull, Graham F.
    • Dedrick, Rebekah M.
    • Mavrich, Travis N.
    • Garlena, Becky
    Description

    This dataset contains twelve high throughput sequenced gene expression profiles of mycobacterium smegmatis infected with (1) mycobacteriophage D29 at 15min, 30min, 60min, and 150min, (2) mycobacteriophage StarStuff itself and at 15min, 30min, 60min, and 150min, and (3) mycobacteriophage L5 itself and at 30min and 150 min. Total RNA was isolated, depleted of rRNA, and library prepped.

    Keywords
    • Bacteriophage evolution
    • Evolution, Molecular
    • Gene Expression Profiling
    • Mycobacterium
    • Sequence Analysis, RNA
    Access Rights
    Free to all
  • Internal Dataset

    Data from: Defining housekeeping genes suitable for RNA-seq analysis of the human allograft kidney biopsy tissue

    Authors
    • Wang, Zijie
    • Randhawa, Parmjeet
    Description

    This study used nine different normalization methods to derive housekeeping genes from a RNA-seq data set of 47,611 transcripts derived from 30 biopsies. The biopsies were collected in a variety of clinical settings, with 5 replicates each: normal function, acute tubular injury, acute rejection, interstitial nephritis, interstitial fibrosis/tubular atrophy, and polyomavirus nephropathy. Transcripts...

    Keywords
    • Allografts
    • Biopsy
    • Housekeeping Genes
    • Kidney
    • Sequence Analysis, RNA
    • Transplantation, Kidney
    Timeframe
    2018
    Access Rights
    Free to all
  • Internal Dataset

    Data from: Relaxin reverses inflammatory and immune signals in aged hearts

    Authors
    • Martin, Brian
    • Gabris-Weber, Beth Ann
    • Romero, Guillermo
    • Chattopadhyay, Ansuman
    • 1 more author(s)...
    Description

    Examination of effect of Relaxin (RLX) treatment on young (9-month) and aged (24-month) rats to test the hypothesis that RLX acts at a genomic level to reverse maladaptive remodeling in aging and heart failure. Treatment was 0.4 mg/kg/day RLX for 2-weeks delivered by subcutaneous osmotic mini-pumps or with sodium acetate (controls). There are twenty-one NCBI GEO records, 4 female and 3 male each...

    Keywords
    • Aging
    • Atrial Fibrillation
    • Biomarkers
    • Cardiovascular Diseases
    • Heart Failure
    • Inflammation
    • Macrophage
    • Relaxin
    • Sequence Analysis, RNA
    Access Rights
    Free to all
  • Internal Dataset

    All of Us Research Hub

    Description

    With an emphasis on reaching historically underrepresented populations, the datasets from the All of Us Research Program include: Electronic health records (OMOP CDM used to standardize all EHR data) Biosamples (blood, urine, and saliva) Mobile health data (from wearable devices that may track biometric data like heart rate and blood pressure) Physical measurements (height, weight, BMI,...

    Keywords
    • Cohort Studies
    • Demography
    • Electronic Health Records
    • Health Status
    • Healthcare Disparities
    • Population Characteristics
    • Populations, Underserved
    • Public Health Surveillance
    • Risk Factors
    • Vulnerable Populations
    • Whole Genome Sequencing
    Timeframe
    2017 – Present
    Access Rights
    Free to all
    Application required
    Fee required
  • Internal Dataset

    Data from: SARS-CoV-2 Infections - Gene Expression Omnibus (GEO) Data Mining, Pathway Enrichment Analysis, and Prediction of Potentially Repurposable Drugs

    Authors
    • Chaparala, Srilakshmi
    • Iwema, Carrie L.
    • Chattopadhyay, Ansuman
    Description

    This project describes a protocol to analyze publicly available transcriptomic data from the NCBI Gene Expression Database (GEO) using in silico approach. This involved identifying SARS-CoV-2 infection-induced differentially Expressed (DE) genes from human gene mapping and viral mapping, statistically enriched pathway associations, and potentially repurposable drugs for COVID-19 treatment. Further...

    Keywords
    • COVID-19
    • Gene Expression Profiling
    • SARS-CoV-2
    • Sequence Analysis, RNA
    • Transcriptomics
    • Virus Diseases
    Access Rights
    Free to all
  • Internal Dataset

    MutantHuntWGS

    Authors
    • Ellison, Mitchell A.
    • Walker, Jennifer L.
    • Ropp, Patrick J.
    • Durrant, Jacob D.
    • 1 more author(s)...
    Description

    This Github repository contains a bioinformatics pipeline for identification and characterization of mutations in Saccharomyces cerevisiae. MutantHuntWGS compares data, input in FASTQ format, from a mutant strain to a wild-type strain to identify high confidence sequence variants present only in the mutant. To enable quick and easy installation and to ensure reproducibility, MutantHuntWGS was...

    Keywords
    • Saccharomyces cerevisiae
    • Sequence Alignment
    • Variant Calling
    • Whole Genome Sequencing
    Access Rights
    Free to all
  • Internal Dataset

    Targeted deletion of astrocytic Nhe1 stimulates Wnt/β-catenin-mediated BBB repair and angiogenesis after ischemic stroke

    Authors
    • Begum, Gulnaz
    • Sun, Dandan
    • Chattopadhyay, Ansuman
    • Chaparala, Srilakshmi
    Description

    Examination of effect of deletion of astrocytic Na+/H+ exchanger isoform 1 (Nhe1) on post-stroke recovery and vascular repair. Expression profiling by high throughput sequencing of astrocytes from Gfap-CreERT2+/-;Nhe1f/f mouse brains, 24 hours after transient middle cerebral artery occlusion. Twelve NCBI GEO records: 3 samples each from Wild-type and Nhe1 Astro-KO, both contralateral and ipsilateral....

    Keywords
    • Angiogenesis
    • Astrocytes
    • Blood-Brain Barrier
    • Cerebrovascular Circulation
    • Gene Expression Profiling
    • High-Throughput Nucleotide Sequencing
    • Ischemic Stroke
    • Mus musculus
    • RNA-Seq
    Access Rights
    Free to all