title: The microRNA profile of human periodontal ligament-derived stem cells subjected to dynamic tensile strain

status: Public on Sep 28 2014

city: Miami

first: Herman

middle: S

last: Cheung

address: 1201 NW 16th Street

department: Geriatric Research, Education and Clinical Center

institute: Miami Veterans Affairs Medical Center

summary: This study aimed to investigate the microRNA expression profile of mechnically strained human periodontal ligament-derived stem cells, and SurePrint G3 Human v16 miRNA Array (Agilent) was employed as a screening platform. We discovered 39 differentially expressed microRNAs between the stretched and the static control group.

overall_design: Human periodontal ligament-derived stem cells were cultured on elastic silicone membranes and either subjected to a dynamic mechanical strain protocol (2hr, 5% elongation, 0.5Hz) or left undisturbed. Total RNA was collected and extracted by TRIzol. RNA samples with 28S/18S ratios in the range of 1.4 to 1.8 were used for microRNA microarray analysis using the Agilent SurePrint G3 Human v16 miRNA Array Kit. The samples in each group were triplicated.


title: Identification of gene expression logical invariants in Arabidopsis

status: Public on Oct 31 2018

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

country: USA

institute: UCSD

type:
Expression profiling by array
Third-party reanalysis

summary: Numerous gene expression datasets from diverse tissue samples from the plant variety Arabidopsis thaliana have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of all of the publicly available Arabidopsis datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated. We put together a web resource where gene expression relationships can be explored online which helps visualize the logical relationships between genes. We believe that this website will be useful in identifying important genes in different biological context. The web link is http://hegemon.ucsd.edu/plant/.

sample_organism:
Arabidopsis
Arabidopsis thaliana
Brassica napus
Arabidopsis lyrata subsp. petraea
Arabidopsis halleri

overall_design: 5972 published Arabidopsis microarray samples from about 300 series assayed on the GPL198 were re-analyzed. Metadata were derived from GSE69995 and RMA was used to normalize the CEL files.

first: Sonalisa

last: Pandey