|
| Status |
Public on Sep 03, 2010 |
| Title |
Tarsal conjunctiva, GAR_26 |
| Sample type |
RNA |
| |
|
| Source name |
Swab, tarsal conjunctiva, TF
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tarsal conjunctiva
gender: Male
age (years): 5
ethnicity: Manjago
fpc trachoma score: F2/P1/C0
equivalent who simplified trachoma grade: TF
roche ct/ng amplicor pcr value: NEG
ompa copies per swab: 0
disease: trachoma
|
| Treatment protocol |
Swabs from the tarsal conjunctiva of participants with clinical signs (test) and without (control) of acute trachoma were collected into RNA preservative (RNAlater, Ambion, Inc).
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Upper tarsal conjunctival swab total RNA was extracted and purified with the RNeasy Micro-kit (Qiagen Ltd, Crawley, UK).
|
| Label |
Biotin
|
| Label protocol |
cRNA probes were prepared from 100 microg total RNA using two-rounds in vitro transcription with biotin-labeled nucleotides (Affymetrix RNA transcript labelling kits (Affymetrix, Santa Clara, CA)).
|
| |
|
| Hybridization protocol |
Biotinylated complementary RNA (cRNA) targets were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA) and subsequently 10ug of Fragmented biotinylated cRNA was hybridized, according to the manufacturer’s standard protocols, for 16hrs at 45oC.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix confocal laser scanner 3000.
|
| Description |
GAR_26
|
| Data processing |
Data was subjected to QC analysis followed by RMA and is provided as RMA-normalised natural-scale data. RMA was performed using function rmasummary in Bioinformatics Toolbox version 3.4, Matlab version R2009b.
|
| |
|
| Submission date |
Feb 19, 2010 |
| Last update date |
Sep 03, 2010 |
| Contact name |
Martin James Holland |
| E-mail(s) |
Martin.Holland@lshtm.ac.uk
|
| Phone |
+442079272295
|
| Organization name |
London School of Hygiene and Tropical Medicine
|
| Department |
Infectious and Tropical Diseases
|
| Lab |
Clinical Research
|
| Street address |
Keppel Street
|
| City |
London |
| ZIP/Postal code |
WC1E 7HT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL201 |
| Series (1) |
| GSE20430 |
Expression data from Gambian children with and without the clinical signs of active trachoma: HG-focus array |
|
