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Gene Expression Profiles of Head and Neck Squamous Cell Carcinoma (HNSCC) primary tumors

ABSTRACT: 60 fresh frozen HNSCC from the University of North Carolina at Chapel Hill (UNC) were obtained from the UNC Tissue Procurement Facility under an IRB approved protocol. 55 tumor samples were collected from the primary tumor and five tumor samples were collected from a local recurrence at the primary site; one tumor also had a sample of the primary tumor and an associated lymph node metastasis . In addition, we profiled three normal tonsillar epithelium samples that were collected from three pediatric patients following routine tonsillectomy and four HNSCC tumor derived cell lines (UNC7, UMSCCA1, CAL27 and JHU022). Each experimental sample (tumor, normal or cell line) was assayed versus a “common reference” sample that was a pool of total RNA derived from 30 of the HNSCC samples. This tumor pool reference strategy has been successfully used in another profiling study. In total, 78 experiments were performed, which utilized three separate preparations of the common reference pool. Keywords = Head and neck cancer Keywords = gene expression profiles Keywords = microarray Keywords: parallel sample

ORGANISM(S): Homo sapiens

PROVIDER: GSE686 | GEO | 2004/03/24

SECONDARY ACCESSION(S): PRJNA87635

REPOSITORIES: GEO

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Gene Expression Profiles of Head and Neck Squamous Cell Carcinoma (HNSCC) primary tumors

Project description:60 fresh frozen HNSCC from the University of North Carolina at Chapel Hill (UNC) were obtained from the UNC Tissue Procurement Facility under an IRB approved protocol. 55 tumor samples were collected from the primary tumor and five tumor samples were collected from a local recurrence at the primary site; one tumor also had a sample of the primary tumor and an associated lymph node metastasis . In addition, we profiled three normal tonsillar epithelium samples that were collected from three pediatric patients following routine tonsillectomy and four HNSCC tumor derived cell lines (UNC7, UMSCCA1, CAL27 and JHU022). Each experimental sample (tumor, normal or cell line) was assayed versus a â??common referenceâ?? sample that was a pool of total RNA derived from 30 of the HNSCC samples. This tumor pool reference strategy has been successfully used in another profiling study. In total, 78 experiments were performed, which utilized three separate preparations of the common reference pool. Keywords = Head and neck cancer Keywords = gene expression profiles Keywords = microarray

2010-06-09 | E-GEOD-686 | biostudies-arrayexpress

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BY_wild_parents

Project description:Expression analysis of BY4716(isogenic to S288c) and a wild isolate collected by R. Mortimer. Each strain was grown in culture 6 independent times and RNA from each culture was isolated. Each of these RNA samples was subjected to a dye-swap pair of arrays (except the "RM11" sample, which only got one array). All arrays used the same pool of reference BY4716 sample. In sample titles, "BY" alone signifies the reference sample and all other strings represent independent cultures. All sample titles are of the form S1-S2. S1 indicates the sample whose signal was read as channel 1 (Cy5 labeling, fluorescence at 635 nm) and S2 as channel 2 (Cy3, 532 nm). Keywords: repeat sample

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Project description:transcription profiling of human head and neck squamous cell carcinoma (HNSCC) samples vs. normal tonsil samples using a self-self hybridization experimental design on two-color arrays. Used to identify differentially expressed genes in tumor/normal samples, and compare the result to that of the same samples using the reference design experimental setting. Keywords: tumor/normal comparison 8 HNSCC tumor samples and 8 normal tonsil samples. Each was profiled using a self-self hybridization design, where two aliquots of the same sample were labeled with two different dyes (cy3 and cy5) and hybridize to the same array.

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BYxwild_40

Project description:Expression analysis of F1 haploid segregants from a cross between BY4716 (isogenic to S288c) and a wild isolate collected by R. Mortimer. Each segregant sample was subjected to a dye-swap pair of arrays. All arrays used the same pool of reference BY4716 sample. In sample titles, "BY" alone signifies the reference sample and all other strings represent segregants. All sample titles are of the form S1-S2. S1 indicates the sample whose signal was read as channel 1 (Cy5 labeling, fluorescence at 635 nm) and S2 as channel 2 (Cy3, 532 nm). Keywords: repeat sample

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Rat diaphyseal femoral fracture healing: Plate fixation vs. intramedullary nail

Project description:This is a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery. The sham surgery group received a surgical exposure of the femur, but no fracture, no plate, and no nail. Samples were collected at 1 day, 3 days, 1 week, 2 weeks, 4 weeks, and 6 weeks after surgery. Each sample is a pool of RNA from three rats from the same surgery group at the same time point after fracture. The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements. Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw. The no fracture sample was a time 0 control collected on the day of surgery from intact rats. Keywords = rat Keywords = fracture Keywords = plate Keywords = nail Keywords = time Keywords = femur Keywords: time-course

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