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Sample GSM237078 Query DataSets for GSM237078
Status Public on Nov 01, 2007
Title African endemic Kaposi's sarcoma
Sample type SAGE
Anchor NlaIII
Tag Count 48497
Tag Length 10
 
Source name Endemic Kaposi's sarcoma tissue
Organism Homo sapiens
Characteristics 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.
 
Submission date Oct 12, 2007
Last update date Nov 19, 2008
Contact name Antoinette van der Kuyl
E-mail(s) a.c.vanderkuyl@amc.uva.nl
Phone 31 20 5666778
Organization name Academic Medical Centre, University of Amsterdam
Department Human Retrovirology
Street address
City Amsterdam
ZIP/Postal code 1105 AZ
Country Netherlands
 
Platform ID GPL4
Series (1)
GSE514 AIDS-related Kaposi's sarcoma

Data table header descriptions
TAG
COUNT
TPM tags per million

Data table
TAG COUNT TPM
AATTTTTTTT 1 20.62
TTATTTTTTT 1 20.62
TTGTTTTTTT 1 20.62
GGCTTTTTTT 4 82.48
ATAATTTTTT 1 20.62
TGAATTTTTT 1 20.62
CACATTTTTT 1 20.62
GTGGTTTTTT 1 20.62
GGCCTTTTTT 3 61.86
AATTATTTTT 1 20.62
CTATATTTTT 1 20.62
TAATATTTTT 3 61.86
TGGTATTTTT 1 20.62
GATAATTTTT 1 20.62
GAGAATTTTT 2 41.24
CCCAATTTTT 1 20.62
AGTGATTTTT 1 20.62
TTTTGTTTTT 1 20.62
GCTTGTTTTT 1 20.62
CGCTGTTTTT 2 41.24

Total number of rows: 16443

Table truncated, full table size 307 Kbytes.




Supplementary data files not provided

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