|
| Status |
Public on Dec 05, 2015 |
| Title |
JSC1_rep3 |
| Sample type |
other |
| |
|
| Source name |
JSC1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: JSC1
tumour: Primary effusion lymphoma
kshv +/-: +
ebv +/-: +
|
| Extracted molecule |
other |
| Extraction protocol |
All miRNA was isolated using the miracleTM miRNA isolation kit (Stratagene, La Jolla, CA).
|
| Label |
Cy3
|
| Label protocol |
100 ng enriched miRNA (or total RNA for the C666 cell line) was added to the labelling reaction, and the entire reaction was hybridized to the array for 20 hours at 55°C.
|
| |
|
| Hybridization protocol |
100 ng enriched miRNA (or total RNA for the C666 cell line) was added to the labelling reaction, and the entire reaction was hybridized to the array for 20 hours at 55°C.
|
| Scan protocol |
Unnormalised data were extracted using Agilent Feature Extraction software (v9.5.3.1).
|
| Description |
Stratagene enriched for miRNA
|
| Data processing |
R and BioConductor were used to background subtract and scale normalise the data at the probe level. Additionally, we applied a filter to reduce the effect of poorly performing probes on overall probeset intensities. Intensity values were first assembled into specific miRNA probe groups (PGi) and medians calculated for each probe group. The median of the probe group medians was then calculated (PGAll). Probe groups were included where PGi / PGAll was greater than 0.75. This intensity filter was empirically derived to minimise false positive miRNA intensities, for example miRs of herpesviruses that are not present in lymphomas. An overall miRNA intensity value was determined as the mean of the remaining PGi’s.
|
| |
|
| Submission date |
Oct 06, 2009 |
| Last update date |
Dec 05, 2015 |
| Contact name |
Dan Frampton |
| Organization name |
UCL
|
| Department |
Infection
|
| Lab |
Kellam
|
| Street address |
Gower Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9081 |
| Series (2) |
| GSE18437 |
Differentially expressed human and viral miRNAs across a panel of B-cell lines, including primary effusion lymphomas |
| GSE18439 |
Transcription repression of miR-221 leads to p27 expression in PEL |
|
