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Series GSE37717 Query DataSets for GSE37717
Status Public on Jun 11, 2013
Title Conjunctival miRNA expression data in scarring and inflammatory trachoma
Organism Homo sapiens
Experiment type Other
Summary 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.
 
Overall design 63 total Samples. 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.
 
Contributor(s) Derrick T, Roberts C, Rajasekhar M, Burr S, Makalo P, Joof H, Harding-Esch E, Bailey RL, Mabey DC, Burton MJ, Holland MJ
Citation(s) 23516655
Submission date May 02, 2012
Last update date Jun 11, 2013
Contact name Tamsyn Ruth Derrick
E-mail(s) tamsyn.derrick@lshtm.ac.uk
Phone 02079272419
Organization name london school of hygiene and tropical medicine
Street address keppel street
City london
ZIP/Postal code WC1E 7HT
Country United Kingdom
 
Platforms (2)
GPL8979 Applied Biosystems Human Taqman MicroRNA Array v2.0
GPL11316 Applied Biosystems Human Taqman MicroRNA Array v3.0
Samples (69)
GSM925935 Tarsal conjunctiva F-0778 card A
GSM925936 Tarsal conjunctiva F-1217 card A
GSM925937 Tarsal conjunctiva F-1233 card A
Relations
BioProject PRJNA162871

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE37717_fold-change_cardA.txt.gz 11.4 Kb (ftp)(http) TXT
GSE37717_fold-change_cardB.txt.gz 7.9 Kb (ftp)(http) TXT
GSE37717_full_63_Samples_metadata_for_Raw.txt.gz 1.1 Kb (ftp)(http) TXT
GSE37717_non-normalized_cardA.txt.gz 61.2 Kb (ftp)(http) TXT
GSE37717_non-normalized_cardB.txt.gz 39.7 Kb (ftp)(http) TXT
Raw data are available on Series record
Processed data included within Sample table
Processed data are available on Series record

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