Affymetrix GeneChip Human Genome HG-U133A [HG-U133A]

Kaposi sarcoma herpesvirus−induced cellular reprogramming contributes to the lymphatic endothelial gene expression in Kaposi sarcoma

ARID3B Induces Malignant Transformation of Mouse Embryonic Fibroblasts and Is Strongly Associated with Malignant Neuroblastoma

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Identification of the relationships of Kaposi sarcoma (KS), normal skin to various cell cultures. The effects of KS herpes virus, the infectious cause of KS, on infected endothelial cells are also investigated.

Transcription profiling of Kaposi sarcoma, normal skin and primary cells

Kaposi sarcoma herpesvirus-induced cellular reprogramming contributes to the lymphatic endothelial gene expression in Kaposi sarcoma

Identification of the relationships of Kaposi sarcoma (KS), normal skin to various cell cultures. The effects of KS herpes virus, the infectious cause of KS, on infected endothelial cells are also investigated.


Affymetrix:Protocol:ExpressionStat

Title: Affymetrix CHP Analysis (ExpressionStat). Description:

Affymetrix:Protocol:Hybridization-EukGE-WS2v4

Title: Fluidics Station Protocol. Description:

Affymetrix:Protocol:Percentile

Title: Affymetrix CEL Analysis (Percentile). Description:

P-MEXP-3631

5 AIDS-KS from 5 different individuals, 1 classic KS and 5 skin biopsies from 5 different individuals were used for the array studies. All the KS biopsies are nodular lesions that contained over 80% spindle cells. An AIDS-KS cell line, KS Y-1, and an iatrogenic-KS cell line, KS-IMM, were grown in DMEM (Gibco BRL) supplemented with 5% heat-inactivated fetal calf serum. Primary microvascular endothelial cells (MVECs; CC-2543, Clonetics, Walkersville, Md.) and human umbilical vein endothelial cells (HUVECs; CC-2517, Clonetics) were cultured in EGM-2 MV BulletKit medium (CC-3202, Clonetics). Human lymphatic and blood vessel endothelial cells (LECs and BECs) were isolated by a polyclonal podoplanin antibody from 3 different batches of MVECs from 3 different donors and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C as described. Immortalized human endothelial cells (IECs) were cultured in EGM-2 MV BulletKit medium. Primary human uterine and aortic smooth muscle cells (UtSMCs, CC-2652 and AoSMCs, CC-2571, Clonetics) were cultured in SmGM-3 BulletKit medium (CC-3178, Clonetics). Human primary dermal fibroblasts (CC-2511, Clonetics) and 2 primary fibroblasts (CR1E and SS1MB) isolated from biopsies were cultured in FGM-2 MV BulletKit medium (CC-3132, Clonetics). Human bone marrow CD34-negative mesenchymal stem cells and CD34+ stem cells were isolated from 3 different donors. CD34+ cells were directly used for RNA extraction but mesenchymal stem cells were further cultured in MesenCult basal medium (05401; StemCell, Vancouver, Canada) supplemented with mesenchymal stem cell stimulatory supplements (05402; StemCell). Each sample was screened and found to be free from mycoplasma contamination.

P-MEXP-3633

Skin samples and KS biopsies were fresh frozen in liquid nitrogen and stored at -70°C until use.

P-MEXP-3634

P-MEXP-3636

P-MEXP-3687

RMA log expression units (Nucleic Acids Res 2003 31:e15) were calculated from Affymetrix GeneChip array data (.CEL files; Nat Biotechnol 1996 14:1675-80) using the Bioconductor package (www.bioconductor.org) for the R statistical programming language (www.r-project.org). In brief, each group of arrays was background corrected using the RMA model-based background correction on perfect-match probes only (see above (RMA) reference for further details). Arrays were subsequently normalized using the quantile normalization method and probe set data was summarized using a median polish.

P-MEXP-3764

Primary cells and 2 KS cell lines are cultured on 10-cm petri dishes till confluency and then lysed by the lysis buffer in the RNeasy Mini kit as described in the extraction protocol. CD34+ bone marrow cells were directly used for RNA extraction after isolation without any culture.

Transcription profiling of Kaposi sarcoma, normal skin and primary cells

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