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Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human breast cancer or Dukes B colon cancer samples to compare the outcome from those fresh frozen and those stored in RNAlater preservative

ABSTRACT: A number of breast or colon specific genes predictive of the relapse status were used in comparing the outcome from matched fresh frozen and stored in RNAlater preservative. Experiment Overall Design: 31 pairs of matched breast and 21 pairs of matched colon primary tumors either fresh frozen or stored in RNAlater preservative

ORGANISM(S): Homo sapiens

DISEASE(S): lymph node-negative breast cancer

SUBMITTER: Jack Yu

PROVIDER: E-GEOD-3726 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Prognostic gene expression signatures can be measured in tissues collected in RNAlater preservative.

Chowdary Dondapati D Lathrop Jessica J Skelton Joanne J Curtin Kathleen K Briggs Thomas T Zhang Yi Y Yu Jack J Wang Yixin Y Mazumder Abhijit A

The Journal of molecular diagnostics : JMD 20060201 1

Gene expression signatures have the ability to serve in both prognostic and predictive capacities in patient management. The use of RNA as the starting material and the lability of this analyte, however, dictate that tissues must be snap-frozen or stored in a solution that can maintain the integrity of the RNA. We compared pairs of snap-frozen and RNAlater preservative-suspended tissue from 30 such paired lymph node-negative breast tumors and 21 such paired Dukes' B colon tumors. We assessed the ...[more]

PMID: 16436632

Similar Datasets

Prognostic gene signatures can be measured with samples stored in RNAlater

Project description:A number of breast or colon specific genes predictive of the relapse status were used in comparing the outcome from matched fresh frozen and stored in RNAlater preservative. Keywords: disease state analysis

2005-12-06 | GSE3726 | GEO

Simple ambient preservation of human tissues for RNA expression array analysis

Project description:We used quantitative RNA expression profiling on the Affymetrix U133 human expression array to validate quantitative expression results obtained with the tissue preservative RNALater against snap frozen and fresh tissues as a means of routine tissue collection and temporary storage. By using split samples from a homogenous tissue (uterine myometrium), and including duplicates within each processing group compared, we were able to undertake a formal ANOVA analysis comparing the magnitude of result variation contributed by sample source (different patients), processing protocol (fresh vs. frozen vs. 24 or 72 hours RNALater), and random background (duplicates). The dataset was randomly permuted to define a baseline pattern of test statistic values against which the observed results could be interpreted. Ambient storage of tissues for 24 or 72 hours in RNALater did not contribute any systematic shift in quantitative RNA expression results relative to the alternatives of fresh or frozen tissue. Keywords: parallel sample

2004-04-09 | GSE1296 | GEO

Transcription profiling of fresh, frozen and RNALater preserved human uterine myometrium samples

2007-06-21 | E-GEOD-1296 | biostudies-arrayexpress

Comparative proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies

Project description:Clinical proteomics research is in part limited by the availability of clinical samples. However, large biobanks exist worldwide containing formalin-fixed and paraffin embedded samples and samples stored in RNAlater. The extraction of proteins for proteome analysis from samples prepared by either method has been demonstrated. However, the impact of the preservation method on the result of a quantitative proteome analysis remains largely uninvestigated. We, therefore, conducted a proteome analysis of human colon mucosal biopsies where the material had been preserved accordingly. Twenty-four colon mucosal biopsies were extracted from the sigmoideum by endoscopy from two participants. The biopsies were either directly-frozen, stabilized in RNAlater, or stabilized by formaldehyde fixation immediately or incubated for 30 min to simulate a clinical situation, followed by paraffin embedding. The impact of the preservation method on the result of a proteome analysis was characterized by high throughput gel free quantitative proteomics.

2015-11-23 | PXD002029 | Pride

Gene expression analysis of lung cancer using long time stored formalin-fixed and paraffin embedded (FFPE) tissue

Project description:This study was performed to evaluated RNA extraction and gene expression analysis of FFPE specimen stored for more than 20 years. Using long time stored FFPE material; large retrospective studies correlating molecular features with therapeutic response and clinical outcome, can be performed. Quantitative PCR (qPCR) was used to evaluate RNA extraction methods and to compare gene expression profiles of FFPE and fresh frozen (FF) tissue. Extracted RNA was subsequently subjected to microarray analysis and compared to qPCR data. The Ambion RecoverAll kit appears to be particularly suited for RNA extraction of long time stored FFPE tissues. Gene expression analysis using Affymetrix platform displayed a high degree of correlation for endogenous control genes comparing FF and FFPE tissues. We conclude that high quality gene expression signatures can be recognized using Affymetrix gene expression platform on FFPE tissue stored for more than 20 years. However, a general interpretation must be done with caution as different FFPE procedures have varying effects on RNA quality.

2011-09-15 | GSE31735 | GEO

Comparison of Nanostring nCounter data on FFPE colon cancer samples and Affymetrix microarray data on matched frozen tissues

2015-10-27 | GSE62932 | GEO

Expression data from 5 colorectal cancer patients neoadjuvantly treated with Imatinib (ImPACCT study)

Project description:Gene expression profiling of CMS4 colon cancer treated with Imatinib in the ImPACCT study. Fresh-frozen biopsies were taken during diagnostic colonoscopy for CMS4 identification. Five patients gave informed consent for two week of neoadjuvant Imatinib therapy prior to removal of the primary tumor. Fresh-frozen samples were taken from surgically resected colon cancer specimens.

2022-06-01 | GSE196263 | GEO

Expression data from melanosis coli (MC)

Project description:There is still a big debate about the correlation between melanosis coli (MC) and carcinoma. We used HTA2.0 to investigate the expression changes of lncRNAs and mRNAs in human colonic mucosa with or without MC and try to investigate MC from gene aspect, eventually to demonstrate whether thereâs a certain correlation between MC and carcinoma. GeneChipÂ® Human Transcriptome Array 2.0 (HTA 2.0) microarrays were adopted. The expression profile of lncRNAs and mRNA were tested in five colon tissue biopsy specimen of MC patients and five demographically-matched controls. This study recruited a total of five MC patients and five coupled matched controls. All specimens were obtained from colonoscopy. The fresh specimens of colon tissues form MC patients and control patients were washed with RNAase free water and put into RNAlater (Qiagen) immediately and frozen in -80Â°C. Gene Ontology (GO) and KEGG Pathway analyses of aberrantly expressed mRNAs were performed to identify the related biological functions and pathologic pathways.

2016-05-30 | E-GEOD-78933 | biostudies-arrayexpress

Repetition of comparison of sample preservation methods for field collection of animal-microbe symbioses for metaproteomic analyses

Project description:When studying gene expression in microbe-animals symbioses collected in the field it is essential to quickly and efficiently preserve in situ symbiont and host protein abundance patterns. One of the most commonly used sample preservation methods for samples targeted for proteomic analyses is flash freezing, however, liquid nitrogen or dry ice needed for flash freezing are often not available at remote field sites. We replicated our experiment from PXD014591 to test if RNAlater allows preserving proteins in animal-microbe symbioses as efficiently as flash freezing and without introducing issues with downstream processing. We used the marine gutless oligochaete Olavius algarvensis as a model for testing. Olavius algarvensis lives in shallow water sediments off the coast of Elba, Italy. It has no digestive and excretory system and harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (Kleiner et al., 2012, PNAS 109(19):1173-82). We compared six RNAlater preserved and eight flash frozen samples in terms of the number of identified proteins, abundances of individual proteins and potential biases against specific protein or taxonomic groups. Six worms were incubated in RNAlater for 24 hours. After incubation, RNAlater was removed and samples were stored at -80°C. Eight worms were directly flash frozen in liquid nitrogen and stored at -80 °C immediately after preservation.

2021-11-03 | PXD026631 | Pride

Comparison of Nanostring nCounter data on FFPE colon cancer samples and Affymetrix microarray data on matched frozen tissues

Project description:The prognosis of colorectal cancer (CRC) stage II and III patients is still a challenge due to the difficulties of finding robust biomarkers and assays. The majority of published gene signatures of CRC have been generated on frozen colorectal tissues. Because collection of fresh frozen tissues is not routine and the quantity and quality of RNA derived from formalin-fixed paraffin-embedded (FFPE) tissues is vastly inferior to that derived from fresh frozen tissue, a clinical test for improving staging of colon cancer will need to be designed for FFPE tissues in order to be widely applicable. We have designed a custom Nanostring nCounter assay for quantitative assessment of expression of 414 gene elements consisting of multiple published gene signatures for colon cancer prognosis, and systematically compared the gene expression quantification between nCounter data from FFPE and Affymetrix microarray array data from matched frozen tissues using 414 genes. For microarray studies, representative sections of fresh tissue specimens were flash frozen in liquid nitrogen and stored at â80Â°C until RNA isolation. RNA was purified from tissue sections containing >80% epithelial tumor tissue using RNeasy (QIAGEN, Valencia, CA) according to manufacturerâs instructions. Samples were hybridized to Affymetrix arrays Human Genome U133 Plus 2.0 GeneChip Expression Arrays, Santa Clara, CA). The samples included four healthy control patient tissues, 12 stage I, 17 stage II, 20 stage III and 15 stage IV CRC patient tissues. Please note that only the *matched.csv files containing matched 414 genes' microarray and nanostring data are provided without the nanostring experimental descriptions. The matching samples between GSE62932 and the Nanostring study are indicated in the matching_samples.txt.

2015-10-27 | E-GEOD-62932 | biostudies-arrayexpress

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