Library constructed from mixed frozen biopsies from nodal Kaposi's sarcoma (KS) lesions from four HIV-1 negative male African endemic KS patients. Two patients were from Zaire, one patient was from Mali, and the fourth patient originated from Cameroon. All four skin biopsies showed a similar histopathological picture of nodular advanced-stage Kaposi’s sarcoma with irregular, dense areas of spindle cell proliferations that were HHV8-LANA positive.
Biomaterial provider
Celeste Lebbé, Department of Dermatology, Centre Hospitalier Universitaire Saint-Louis, Paris, France
Treatment protocol
The biopsies were cut with a microtome in 10-14 micrometer sections for RNA isolation.
Growth protocol
All tissues were collected, snap frozen, and stored at -80ºC.
Extracted molecule
polyA RNA
Extraction protocol
The SAGE library was constructed from the four pooled tissues using the I-SAGE kit™ from Invitrogen (Carlsbad, CA, USA).
Description
The presence of HHV-8 DNA in the endemic KS lesions was tested with a nested HHV-8 PCR before generation of the SAGE library. Subsequently, the absence of HIV-1 RNA in the endemic KS lesions was tested with a HIV-1 specific RT-PCR before generation of the SAGE library.
Data processing
Primary analysis of the SAGE library was performed with USAGE version2 (van Kampen, A. H., van Schaik, B. D., Pauws, E., Michiels, E. M., Ruijter, J. M., Caron, H. N., Versteeg, R., Heisterkamp, S. H., Leunissen, J. A., Baas, F., & van der Mee, M. (2000). USAGE: a web-based approach towards the analysis of SAGE data. Bioinformatics., 16, 899-905).The program performs initial analyses on raw sequence data, e.g. ditag and tag extraction, tag counting, and tag identification. Tags were identified with the SAGEmap database available through NCBI, to which USAGE is directly linked. Viral tags were identified with a USAGE viral database created by extracting relevant SAGE tags from all viral cDNA sequences present in the NCBI database. Reference: van der Kuyl AC, van den Burg R, Zorgdrager F, Lebbé C, and Cornelissen M. Chapter VIII. Analysis of gene family expression in African endemic- and AIDS-related Kaposi’s sarcoma. Pp. 147-173, In: New Topics in Cancer Research (Horizons in Cancer Research, Volume 34). Ed. FG Drabell. 2006. Nova Science Publishers Inc., Hauppauge NY, USA.
