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Transcription profiling by array of human melanoma xenograft development after propranolol treatment - part1

ABSTRACT: We investigated the effect of a daily propranolol treatment (0.5mg/mL in the water bottle) on human melanoma xenografts development and the subsequent transcriptomic variations

ORGANISM(S): Homo sapiens

SUBMITTER: Wrobel Ludovic

PROVIDER: S-ECPF-MTAB-2404 | biostudies-other |

REPOSITORIES: biostudies-other

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Transcription profiling by array of human melanoma xenograft development after propranolol treatment - part 2

Project description:We investigated the effect of a daily propranolol treatment (0.5mg/mL in the water bottle) on human melanoma xenografts development and the subsequent transcriptomic variations

| S-ECPF-MTAB-2405 | biostudies-other

Transcription profiling by array of human HhAntag-treated pancreatic xenograft tumors

Project description:Four vehicle-treated and four HhAntag-treated pancreatic xenograft tumors were profiled for gene expression changes using Affymetrix U133 Plus 2.0 and Affymetrix Mouse Genome 430 2.0 arrays. Keywords: comparative gene expression, hedgehog, hh A primary human pancreatic tumor xenograft (1051178-A) was established by direct implantation of surgical material into female CD1 nu/nu mice of 6-8 weeks of age. Tumors were serially passaged into larger cohorts of mice for efficacy testing and subsequently distributed into tumor volume-matched cohorts upon tumors reaching between 200 to 350 mm3. HhAntag was resuspended in 0.5% methyl-cellulose, 0.2% Tween-80 (MCT) and administered orally twice daily at 75 mg/kg from a 10 mg/ml suspension. MCT alone served as vehicle control. Tumor xenografts (4/group) were excised following 21 days of dosing and RNA was extracted. Preparation of complementary RNA, Human Genome U133 Plus 2.0 array and Mouse Genome 430 2.0 array hybridizations, and subsequent data analysis were carried out using Affymetrix protocols, with signal intensities being determined by the MAS5.0 algorithm.

| S-ECPF-GEOD-11981 | biostudies-other

Transcription profiling by array of human melanoma cell lines

Project description:Expression profiles of 17 melanoma cell lines were analysed to identify genes differentially expressed between cell lines harbouring wild-type or mutant p16INK4A. Relevant paper: Pavey et al. (2007). Note: all of these cell lines contained wild-type p14ARF, so that the transcriptional effects of p16INk4A could be determined without interference from p14ARF. Experiment Overall Design: The aim of this study was to identify genes which are transcriptional targets of p16INK4A in melanoma.

| S-ECPF-GEOD-7153 | biostudies-other

Transcription profiling by array of human melanoma-derived cell lines after treatment with temozolomide

Project description:To identify patterns of gene expression that correlate with response to treatment with either melphalan or temozolomide we measured both gene expression using microarray genechips and response to drug using a standard in vitro cell proliferation assay. Senstivity to melphalan was measured 48hrs after drug treatment while sensitivity to temozolomide was measured 12 days after drug treatment. Experiment Overall Design: For each of the 50 melanoma-derived cell lines, 1 flask of cells was grown to 80% confluence and harvested for RNA isolation. Cells were lysed in buffer with 1% β-mercaptoethanol and RNA isolated using Qiagen RNeasy-plus RNA isolation kit which included a step to eliminate genomic DNA. RNA concentration was measured and quality assessed using the NanoDrop ND100 spectrophotometer. RNA was reverse transcribed and biotin-labeled cRNA synthesized. The product was hybridized to the Affymetrix human genechip HU133 Plus2 according to manufacturer's instructions. Data was initially assessed for quality and a relative value for expression was calculated as the difference between the perfect match and the mismatch signal intensities using the Affymetrix GeneChip Operating System (GCOS). A detection call (present, absent or marginal) as well as a detection p-value was also calculated. Data was normalized by multiplying each signal by a scaling factor such that the mean signal intensity for each GeneChip was equal to 500. Scaling factors were all under 10.

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Transcription profiling by array of human melanoma cell lines after treatment with 2-deoxy-5-azacytidine

Project description:Melanoma progression model:DAC-mediated gene expression

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Transcription profiling by array of human in-transit extremity melanoma II lesions

Project description:An evaluation of biopsies from patients with in-transit extremity melanoma who have been treated with melphalan in the setting of isolated limb infusion Gene expression profiles were obtained from 52 lesions across 28 patients and evaluated for expression values that correlated with response to melphalan isolated limb infusion Chemotherapy response analysis: complete response - CR; partial response - PR; stable disease - SD; progressive disease - PD. 52 samples.

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Transcription profiling of human H69 xenograft tumors in mice following PDT treatment

Project description:The response of tumors to PDT treatment is expected to provide information on effects of oxygen depletion, induced apoptosis, induction of an inflammatory response and induction of an ani-tumor immune response. Experiment Overall Design: NCI-H69 human SCLC xenografts were induced in SCID mice. Three pairs of xenograft tumors, PDT treated and untreated controls, were harvested four hours after PDT treatment. RNA was isolated and prepared for hybridization to human Affymetrix GeneChip arrays.

| S-ECPF-GEOD-8920 | biostudies-other

Transcription profiling by array of human melanoma cell lines to investigate gene expression

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Project description:Nine heterogeneous melanoma cell lines including D10 and WM115 were studied for cancer stem cell characteristics in vitro. D10 cell line was the only cell line expressing the cancer stem cell marker CD133. Thus, gene expression profiling on CD133+ and CD133- D10 cells was carried out using Affymetrix GeneChips Human Genome U133A 2.0.

| S-ECPF-MEXP-3542 | biostudies-other

Transcription profiling by array of human xenograft laboratory models and primary tumors of small cell lung cancer

Project description:Gene expression was measured on the Affymetrix platform in primary xenografts, xenograft-derived cell lines, secondary xenografts, normal lung, and primary tumors obtained from chemotherapy naive Small Cell Lung Cancer (SCLC). The SCLC primary xenografts were serially propagated in vivo in immunodeficient mice. Cell lines were derived from each xenograft and grown for 6 months using conventional tissue culture conditions. Secondary xenografts were obtained from cell cultures by re-implantation in immunodeficient mice. Such SCLC laboratory models were analyzed along with conventional SCLC cell lines and the derivative secondary xenografts, with normal lung and primary tumors, to assess irreversible gene expression changes induced by culturing conditions. Experiment Overall Design: SCLC primary xenografts were compared to the corresponding xenograft-derived cell lines, and to the secondary xenografts established from the cell lines using the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. Gene expression from SCLC primary tumors was measured using the Affymetrix GeneChip Human Genome U133A 2.0 Array. 3 datasets: GSM380476-GSM380512, GSM380513-GSM380516, and GSM380517-GSM380520

| S-ECPF-GEOD-15240 | biostudies-other

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