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.
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...
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...
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,...
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...
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....
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...