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Transcription profiling of normal amplified samples from cancer patients vs. a common reference (part of a set of 5 experiments

ABSTRACT: Breast tissue normal. BC-N denotes non-tumor breast tissue samples from breast cancer patients, BC-NRm denotes normal breast tissue samples from reduction mammoplasties.

ORGANISM(S): Homo sapiens

SUBMITTER: Nicolau M

PROVIDER: S-ECPF-SMDB-3961 | biostudies-other | 2007 Apr

REPOSITORIES: biostudies-other

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Transcription profiling of normal amplified samples from cancer patients vs. a common reference (part of a set of 5 experiments

Project description:Breast tissue normal. BC-N denotes non-tumor breast tissue samples from breast cancer patients, BC-NRm denotes normal breast tissue samples from reduction mammoplasties.

2007-03-07 | E-SMDB-3961 | biostudies-arrayexpress

HNSCC samples vs. normal tonsil samples: reference design

2009-01-22 | GSE13398 | GEO

Block Design with Common Reference Samples Enables Robust Large-Scale Label-Free Quantitative Proteome Profiling.

Project description:Label-free quantitative proteomics has become an increasingly popular tool for profiling global protein abundances. However, one major limitation is the potential performance drift of the LC-MS platform over time, which, in turn, limits its utility for analyzing large-scale sample sets. To address this, we introduce an experimental and data analysis scheme based on a block design with common references within each block for enabling large-scale label-free quantification. In this scheme, a large number of samples (e.g., >100 samples) are analyzed in smaller and more manageable blocks, minimizing instrument drift and variability within individual blocks. Each designated block also contains common reference samples (e.g., controls) for normalization across all blocks. We demonstrated the robustness of this approach by profiling the proteome response of human macrophage THP-1 cells to 11 engineered nanomaterials at two different doses. A total of 116 samples were analyzed in six blocks, yielding an average coverage of 4500 proteins per sample. Following a common reference-based correction, 2537 proteins were quantified with high reproducibility without any imputation of missing values from 116 data sets. The data revealed the consistent quantification of proteins across all six blocks, as illustrated by the highly consistent abundances of house-keeping proteins in all samples and the high levels of correlation among samples from different blocks. The data also demonstrated that label-free quantification is robust and accurate enough to quantify even very subtle abundance changes as well as large fold-changes. Our streamlined workflow is easy to implement and can be readily adapted to other large cohort studies for reproducible label-free proteome quantification.

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HNSCC samples vs. normal tonsil samples: reference design

Project description:transcription profiling of human head and neck squamous cell carcinoma (HNSCC) samples vs. normal tonsil samples using a two-color reference design experimental setting. Used to identify differentially expressed genes in tumor/normal samples, and compare the result to that of the same samples using the self-self hybridization experimental setting. Keywords: tumor/normal comparison 8 HNSCC tumor samples and 8 normal tonsil samples. One sample per array. Two-color reference design with a common reference sample (a modified version of the Stratagene Human Universal Reference) on each array.

2010-05-06 | E-GEOD-13398 | biostudies-arrayexpress

Transcriptional profiling of HCC vs. Normal liver and Pericancer vs. Normal liver.

Project description: Not available

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Transcription profiling by array of 178 human breast cancer biopsy samples vs normal breast reference total RNA (Clontech) to identify exons associated with higher risk of relapse

Project description:We profiled breast cancer samples with exon arrays (244K Agilent Human exon) in order to identify exons associated with higher risk of relapse. This set contain 178 single dual color of samples (biopsies) versus normal breast reference (Normal breast Clontech) , 5 dye-swap (10 hybridizations) and 5 self self for controls.

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Statistical inference from multiple iTRAQ experiments without using common reference standards.

Project description:Isobaric tags for relative and absolute quantitation (iTRAQ) is a prominent mass spectrometry technology for protein identification and quantification that is capable of analyzing multiple samples in a single experiment. Frequently, iTRAQ experiments are carried out using an aliquot from a pool of all samples, or "masterpool", in one of the channels as a reference sample standard to estimate protein relative abundances in the biological samples and to combine abundance estimates from multiple experiments. In this manuscript, we show that using a masterpool is counterproductive. We obtain more precise estimates of protein relative abundance by using the available biological data instead of the masterpool and do not need to occupy a channel that could otherwise be used for another biological sample. In addition, we introduce a simple statistical method to associate proteomic data from multiple iTRAQ experiments with a numeric response and show that this approach is more powerful than the conventionally employed masterpool-based approach. We illustrate our methods using data from four replicate iTRAQ experiments on aliquots of the same pool of plasma samples and from a 406-sample project designed to identify plasma proteins that covary with nutrient concentrations in chronically undernourished children from South Asia.

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Neuroblastoma: MYCN normal vs. MYCN amplified

Project description:To evaluate the expression of genes associated with MYCN in NB, 10 tumors with MYCN amplification and 10 with normal MYCN copy number were subjected to oligonucleotide microarray using Agilent oligo microarray chips.

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Transcription profiling of human oral sqamous cell carcinoma patients vs normal samples to associate gene expression profiles and tumor invasion

Project description:There are limited studies attempting to correlate the expression changes in oral squamous cell carcinoma with clinically relevant variables. We determined the gene expression profile of 16 tumor and 4 normal tissues from 16 patients by means of Affymetrix Hu133A GeneChips. The hybridized RNA was isolated from cells obtained with laser capture microdissection, then was amplified and labeled using T7 polymerase-based in vitro transcription. The expression of 53 genes was found to differ significantly (33 upregulated, 20 downregulated) in normal versus tumor tissues under two independent statistical methods. The expression changes in four selected genes (LGALS1, MMP1, LAGY, and KRT4) were confirmed with reverse transcriptase polymerase chain reaction. Two-dimensional hierarchical clustering of the 53 genes resulted in the samples clustering according to the extent of tumor infiltration: normal epithelial tissue, tumors less than or equal to 4 cm in dimension, and tumors more than 4 cm in dimension (P=0.0014). The same pattern of clustering was also observed for the 20 downregulated genes. We did not observe any associations with lymph node metastasis (P=0.097). Experiment Overall Design: We performed microarray analysis using RNA from OSCC cells obtained with LCM from 16 patients and compared these results with 4 control squamous cell epithelium samples.We identified expression profiles of differentially expressed genes between normal and tumor tissues and found that tumor invasiveness of a tumor is highly correlated with its gene expression profile.

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Transcription profiling of human grade 3 invasive ductal carcinomas vs. a common reference differentiates distinct subtypes of grade 3 invasive ductal carcinoma

Project description:Comparison of multiple grade 3 invasive ductal carcinomas arrayed against a common reference.

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