|
| Status |
Public on Sep 30, 2009 |
| Title |
AIDS_KS-biopsy-patient5-repA |
| Sample type |
RNA |
| |
|
| Source name |
AIDS KS lesion biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
tissue: Kaposi sarcoma lesion
patient_replicate: 5
technical_replicate: A
|
| Growth protocol |
Fresh frozen KS and skin biopsies were obtained from the NIH AIDS Cancer Specimen Resource Bank (USA) and from Chelsea and Westminster Hospital (UK). All participants were male, HIV–infected and between the ages of 26 and 58. Three out of five biopsies were collected in London in 2008. The remaining biopsies were nodular stage KS and collected in the U.S.A in 2003. All participants were undergoing anti-retroviral treatment at the time of collection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was disrupted and homogenized using a mechanical rotor and RNA subsequently extracted using the miRNeasy mini kit (Qiagen) according to manufacturer’s instructions. The small RNA fraction was assessed using the Agilent small RNA Kit. Quality and integrity of the RNA fraction between 6 and 150 nucleotides was quantified using the Agilent 2100 bioanalyzer (Agilent).
|
| Label |
Cy3
|
| Label protocol |
Total RNA was labelled with Cy3 using the Agilent miRNA labelling and reagent kit as per manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Cy3 labelled total RNA was hybridised to Agilent Human miRNA Microarray v1.0 as per manufacturer's instructions.
|
| Scan protocol |
The Agilent Human miRNA Microarray was scanned using the Agilent scanner as per manufacturer's instructions.
|
| Description |
P3_KS
|
| Data processing |
Summary expression text files were created using Agilent Feature Extraction Software. From the summary text files we extracted the median (gMedianSignal) and background signal-(gBGUsed). The arrays were then background corrected using the 'normexp' function of the limma package and quantile normalized to each other.
|
| |
|
| Submission date |
May 31, 2009 |
| Last update date |
Aug 24, 2009 |
| Contact name |
Stephen Henderson |
| E-mail(s) |
[email protected]
|
| Phone |
02076796827
|
| Fax |
02076796851
|
| Organization name |
UCL
|
| Department |
Cancer Institute
|
| Lab |
Viral Oncology
|
| Street address |
Paul O'Gorman Building, Huntley Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL8617 |
| Series (2) |
| GSE16353 |
The profile of cellular and KSHV microRNAs in AIDS_KS biopsies (and normal skin control biopsies) |
| GSE16357 |
Effects of HHV8 infection in lymphatic endothelial cells |
|
