Bovine RNA-seq Data Analysis of Liver and Pituitary Gland
Poster May 12, 2015
Pareek CS12, Smoczynski R12, Dziuba P12, Sikora M12, Golebiewski M2, Blaszczyk P12, Gelfand B3, Yaping F3, Kumar D3.
An experimental design representing young growing bulls of three cattle breeds at three different developmental ages were sequenced in context to bovine body growth and developmental trait using Illumina NextSeq platform. Approximately 40-50 million paired-end reads were obtained per library (n=36). For each tissue, 18 breed-specific and age dependent-specific libraries were sequenced. Using a computational pipeline, tissue-specific transcripts were mapped to bovine reference genome (UMD3.1 assembly). Mapping tools (https://github.com/alexdobin/STAR/releases) was used to align the reads to the reference cattle genome. Results of transcriptome mapping of liver in Polish Red bulls revealed 98.88% mapping reads (400453035 map reads out of 408045666) and transcriptome mapping of pituitary gland in Hereford bulls revealed 97.80% mapping reads (337471226 map reads out of 345069302). However, paired end transcripts of pituitary gland (Hereford) and liver (Polish red) were properly paired @ of 82.22% and 79.56% respectively. Study provides a glimpse into the tissue specific mRNA content of bovine pituitary gland and liver which will eventually facilitate future experimental trait-associated studies to unravel the putative ESTs and/or causal SNPs for bovine body growth and developmental process.
Characterization of a Type 2 diabetes-associated islet-specific enhancer cluster in STARD10 by genome editing of EndoC-βH1 cellsPoster
Genome-wide association studies (GWAS) have identified more than 100 genetic loci associated with type 2 diabetes. The majority of these are located in the intergenic or intragenic regions suggesting that the implicated variants may alter chromatin conformation. This, in turn, is likely to influence the expression of nearby or more remotely located genes to alter beta cell function. At present, however, detailed molecular and functional analyses are still lacking for most of these variants. We recently analysed one of these loci and mapped five causal variants in an islet-specific enhancer cluster within the STARD10 gene locus. Here, we aimed to understand how these causal variants influence b-cell function by alteration of the chromatin structure of enhancer clusterREAD MORE
Psychiatric Risk Gene Cacna1c and Early Life Stress: Potential Gene-Environment interactions?Poster
Early life stress (ELS) is highly associated with development of psychopathology
and mood disorders in adulthood. Genetic studies have identified variation in the gene calcium voltage-gated channel subunit alpha1C (CACNA1C) to increase risk for several psychiatric disorders. This poster assessed the expression of Cacna1c following prepubertal stress.
Correlations among the Toddler Gut Microbiome and Health Status VariablesPoster
Establishment and succession of the human microbiome begins at birth and microbial composition adapts alongside human development and growth. Development of a healthy signature microbial community has significant effects on health.This study followed 18 very low birth weight (VLBW) infants, measured initially in the from Neonatal Intensive Care Unit (NICU), at the age of two to three years old.READ MORE