Microbiota from human conjunctival swabs
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ABSTRACT:
PROVIDER: PRJNA695364 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Raw sequence reads of microbiota from corneal scrapings or conjunctival swabs
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Project description:Raw sequence reads of microbiota from corneal scrapings or conjunctival swabs
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Project description:Genome-wide analysis of dihydrotestosterone (DHT) induced changes in gene expression in immortalized human conjunctival epithelial cells. Analysis of regulation of immortalized human conjunctival epithelial cells by dihydrotestosterone at gene expression level. The hypothesis tested in the present study was that the androgen-eye interaction in ocular surface epithelial cells like conjunctival cells is influenced by androgens through regulation of the expression of multiple genes. Results provide important information of the differential regulation of numerous genes in response to dihydrotestosterone incubation of immortalized human conjunctival epithelial cells.
2011-03-31 | GSE18094 | GEO
Project description:Human conjunctival cell lines are useful tools for modeling ocular surface disease and evaluation of ocular drugs. Here we demonstrate that the IOBA-NHC and the ChWK conjunctival epithelial cell lines show, using an unbiased gene microarray approach, unique gene expression signatures that differ from primary conjunctival epithelial cells (PCEC) and conjunctival tissue. Globally, the expression profile obtained with the Affymetrix U133A chip (>22000 genes) from PCEC was clustered more closely to conjunctival tissue than either of the 2 cell lines. However, when restricted to Gene Ontology sub-categories: cellular defense, viral replication/cycling, antigen presentation, anti-oxidant pathways and ubiquitin ligase complex, the cell lines correlated reasonably well to PCEC (r > 0.70). In the category response to inflammation, correlation of cell lines to PCEC was poor (r = -0.012 and â0.041 for IOBA-NHC and ChWK respectively). In general, the expression profile in IOBA-NHC cells was better correlated to PCEC than the ChWK cells. This was statistically significant (p<0.05) when one considers all the genes on the chip, or for proteins in the extracellular region, response to wounding, stress, lipid, protein and organic acid metabolism, development and differentiation. Our results are useful for the choice of conjunctival cell lines, if necessary, in future experiments, to increase validity of extrapolation to clinical scenarios. Experiment Overall Design: Affymetrix U133A Genechip Experiment Overall Design: Experimental samples: Experiment Overall Design: IOBA-NHC cells (5 samples) Experiment Overall Design: Chang conjunctival epithelial cells WK derivative (4 samples) Experiment Overall Design: Primary conjunctival epithelial cells from explants (3 samples, obtained from cadaveric human explants) Experiment Overall Design: Conjunctival tissue from pterygium study where small piece uninvolved conjunctiva harvested (4 patients' RNA pooled to form one sample, total number of samples: 4) Experiment Overall Design: RT and hybridisation 16 hr according to Affymetrix protocol Experiment Overall Design: Labeling with biotin Experiment Overall Design: Washing microfluidics station 450 Experiment Overall Design: Analysis with Genespring GX 7.3.1 Experiment Overall Design: RMA normalisation following by normalisation to chip level median signal Experiment Overall Design: These processed data used for correlation analysis Experiment Overall Design: Further gene level normalisation to primary conjunctival epithelial cells samples for the purpose of fold change analysis to compare expression in IOBA or ChWK cells vs primary conjunctival epithelial cells.
2008-06-16 | E-GEOD-8633 | biostudies-arrayexpress
Project description:Genome-wide analysis of dihydrotestosterone (DHT) induced changes in gene expression in immortalized human conjunctival epithelial cells. Analysis of regulation of immortalized human conjunctival epithelial cells by dihydrotestosterone at gene expression level. The hypothesis tested in the present study was that the androgen-eye interaction in ocular surface epithelial cells like conjunctival cells is influenced by androgens through regulation of the expression of multiple genes. Results provide important information of the differential regulation of numerous genes in response to dihydrotestosterone incubation of immortalized human conjunctival epithelial cells. Total RNA was obtained from immortalized human conjunctival epithelial cells treated for 96 hours with 10 nM dihydrotestosterone (n=3) or vehicle (n=3). The RNA was then used with Illumina HumanHT-12 v3 Expression BeadChips to determine the effect of DHT on gene expression in an immortalized human conjunctival epithelial cell line developed in Dr. Rheinwald's laboratory [Rheinwald et al. MCB, 22 (14): 5157. (2002)] and charecterized in Dr. Ilene Gibson's laboratory [Gipson et al. IOVS, 44 (6): 2496. (2003)].
2011-03-31 | E-GEOD-18094 | biostudies-arrayexpress
Project description:the middle meatus swabs Raw sequence reads
| PRJNA697755 | ENA
Project description:Ocular infection with Chlamydia trachomatis (trachoma) is the leading cause of blindness that results from infection. Chronic inflammation is believed to drive the scarring process and the progressive blinding disease, however the mechanisms by which this occurs are not completely understood. We hypothesized that Micro RNA (miRNA), as key regulators of genes in inflammatory pathways, are involved in the immunopathogenesis and tissue remodeling observed in trachoma. Conjunctival swabs were collected from a total of 63 individuals resident in trachoma endemic communities in The Gambia, West Africa. MiRNA was extracted from the conjunctival swabs of 23 healthy controls (N), 18 cases with trachomatous scarring (TS) and 22 cases with trachomatous scarring in the presence of clinically significant inflammation (TSI) using Qiagen Allprep DNA/RNA/protein kits. Following reverse transcription and pre-amplification, quantitative RT-PCR was performed using TaqMan Array Human MicroRNA genecards (Av2.0 and Bv3.0) on a 7900HT thermal cycler (Life Technologies, Inc). A total of 754 of the most well characterised unique human miRNA from miRBase (www.mirbase.org/) were screened. Data from each array were uploaded and analysed using the high throughput qPCR package in bioconductor R. Samples with a global miRNA median cycle threshold of 40 were filtered out. A and B cards were analysed separately due to differences in performance of samples on each card. In the A card group 40 samples were normalized and tested: 8 TSI, 16 TS and 16 N. In the B card group 29 samples were normalized and tested: 6 TSI, 13 TS and 10 N. Results were normalized by rank invariant normalization as it reduced the coefficient of variation and increased sample distribution homology more than any other normalization procedure tested. Data in each group were tested for differential expression by Limma.
2013-06-11 | GSE37717 | GEO