Exon Level Expression Profiling: a Novel Unbiased Transcriptome Analysis for Body Fluids
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE7760 | GEO | 2008/05/20
SECONDARY ACCESSION(S): PRJNA99889
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptome analysis of partially degraded and fragmented RNA samples from body fluids Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in body fluids such as saliva, which is accessible, cost-effective, and non-invasive. However, this goal has not been fully realized because saliva, like many clinical samples, contains partially fragmented and degraded RNAs that are difficult to amplify and detect with prevailing technologies. Here, using nanogram scale salivary RNA as a proof-of-principle example, we describe our progress with a novel poly-A tail independent mRNA amplification strategy combined with the Affymetrix GeneChip Exon arrays. We defined a Salivary Exon Core Transcriptome (SECT) with highly similar expression profiles in healthy individuals verified by quantitative PCR. Informatics analysis of SECT provided important mechanistic insight to their potential origin and function. Finally we demonstrated the diagnostic potential of true exon level expression profiling approach with salivary exon biomarkers that accurately discriminated gender in healthy individuals. We analyzed saliva from 18 healthy subjects (7 males, 11 females) using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.
2008-05-19 | E-GEOD-7760 | biostudies-arrayexpress
Project description:This is a pilot study. We are trying to detect potential salivary biomarkers in mice with a pancreatic tumor. Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in body fluids such as saliva, which is accessible, cost-effective, and non-invasive. However, this goal has not been fully realized because saliva, like many clinical samples, contains partially fragmented and degraded RNAs that are difficult to amplify and detect with prevailing technologies. Here, using nanogram scale salivary RNA as a proof-of-principle example, we describe our progress with a novel poly-A tail independent mRNA amplification strategy combined with the Affymetrix GeneChip Exon arrays. We defined a Salivary Exon Core Transcriptome (SECT) with highly similar expression profiles in healthy individuals verified by quantitative PCR. Informatics analysis of SECT provided important mechanistic insight to their potential origin and function. Finally we demonstrated the diagnostic potential of true exon level expression profiling approach with salivary exon biomarkers that accurately discriminated gender in healthy individuals. Recent studies have demonstrated that discriminatory salivary biomarkers can be readily detected upon the development of systemic diseases such as pancreatic cancer, breast cancer, lung cancer and ovarian cancer. However, the utility of salivary biomarkers for the detection of systemic diseases has been undermined due to the absence of biological and mechanistic rationale why distal diseases from the oral cavity would lead to the development of discriminatory biomarkers in saliva. Here, we examine the hypothesis that pancreatic tumor-derived exosomes are mechanistically involved in the development of pancreatic cancer-discriminatory salivary transcriptomic biomarkers. We first developed a pancreatic cancer mouse model that yielded discriminatory salivary biomarkers by implanting the mouse pancreatic cancer cell line Pan02 into the pancreas of the syngeneic host C57BL/6. The role of pancreatic cancer-derived exosomes in the development of discriminatory salivary biomarkers was then tested by engineered a Pan02 cell line that is suppressed for exosome biogenesis, implanted into the C56BL/6 mouse and examine if the discriminatory salivary biomarker profile was ablated or disrupted. Suppression of exosome biogenesis results in the ablation of discriminatory salivary biomarker development. This study supports that tumor-derived exosomes provide a mechanism in the development of discriminatory biomarkers in saliva and distal systemic diseases. We analyzed saliva from 6 healthy mice and 6 mice with a pancreatic tumor using the Affymetrix Mouse Exon Genome 430 2.0 platform. Array data was processed by dChip. No techinical replicates were performed.
2013-06-12 | E-GEOD-47811 | biostudies-arrayexpress
Project description:This is a pilot study. We are trying to detect potential salivary biomarkers in mice with a pancreatic tumor. Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in body fluids such as saliva, which is accessible, cost-effective, and non-invasive. However, this goal has not been fully realized because saliva, like many clinical samples, contains partially fragmented and degraded RNAs that are difficult to amplify and detect with prevailing technologies. Here, using nanogram scale salivary RNA as a proof-of-principle example, we describe our progress with a novel poly-A tail independent mRNA amplification strategy combined with the Affymetrix GeneChip Exon arrays. We defined a Salivary Exon Core Transcriptome (SECT) with highly similar expression profiles in healthy individuals verified by quantitative PCR. Informatics analysis of SECT provided important mechanistic insight to their potential origin and function. Finally we demonstrated the diagnostic potential of true exon level expression profiling approach with salivary exon biomarkers that accurately discriminated gender in healthy individuals. Recent studies have demonstrated that discriminatory salivary biomarkers can be readily detected upon the development of systemic diseases such as pancreatic cancer, breast cancer, lung cancer and ovarian cancer. However, the utility of salivary biomarkers for the detection of systemic diseases has been undermined due to the absence of biological and mechanistic rationale why distal diseases from the oral cavity would lead to the development of discriminatory biomarkers in saliva. Here, we examine the hypothesis that pancreatic tumor-derived exosomes are mechanistically involved in the development of pancreatic cancer-discriminatory salivary transcriptomic biomarkers. We first developed a pancreatic cancer mouse model that yielded discriminatory salivary biomarkers by implanting the mouse pancreatic cancer cell line Pan02 into the pancreas of the syngeneic host C57BL/6. The role of pancreatic cancer-derived exosomes in the development of discriminatory salivary biomarkers was then tested by engineered a Pan02 cell line that is suppressed for exosome biogenesis, implanted into the C56BL/6 mouse and examine if the discriminatory salivary biomarker profile was ablated or disrupted. Suppression of exosome biogenesis results in the ablation of discriminatory salivary biomarker development. This study supports that tumor-derived exosomes provide a mechanism in the development of discriminatory biomarkers in saliva and distal systemic diseases.
2013-06-12 | GSE47811 | GEO
Project description:The ability to predict tissue type and donor’s age from molecular profiles of crime scene samples has practical implications in forensics. In order to identify body fluid- and age-associated DNA methylation changes, genome-wide DNA methylation profiling was carried out for body fluids including blood, saliva, semen, menstrual blood, and vaginal fluid obtained from individuals aged 20 to 59. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in bisulfite converted DNA. Samples included 12 of each blood, saliva and semen samples from 18 male donors aged 20 to 59, and 3 of each vaginal fluid and menstrual blood samples from 4 female donors in their twenties. Genome-wide DNA methylation profiling of body fluids obtained from individuals aged 29 to 41. The Illumina Infinium 450K Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450K CpGs from human body fluids including blood, saliva and semen. Bisulfite converted DNA from the 6 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
2015-05-26 | E-GEOD-59508 | biostudies-arrayexpress
Project description:The ability to predict tissue type and donor’s age from molecular profiles of crime scene samples has practical implications in forensics. In order to identify body fluid- and age-associated DNA methylation changes, genome-wide DNA methylation profiling was carried out for body fluids including blood, saliva, semen, menstrual blood, and vaginal fluid obtained from individuals aged 20 to 59. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in bisulfite converted DNA. Samples included 12 of each blood, saliva and semen samples from 18 male donors aged 20 to 59, and 3 of each vaginal fluid and menstrual blood samples from 4 female donors in their twenties. Genome-wide DNA methylation profiling of body fluids obtained from individuals aged 37 to 48. The Illumina Infinium 450K Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450K CpGs from human body fluids including blood, saliva and semen. Bisulfite converted DNA from the 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
2015-05-26 | E-GEOD-59507 | biostudies-arrayexpress
Project description:The ability to predict tissue type and donor’s age from molecular profiles of crime scene samples has practical implications in forensics. In order to identify body fluid- and age-associated DNA methylation changes, genome-wide DNA methylation profiling was carried out for body fluids including blood, saliva, semen, menstrual blood, and vaginal fluid obtained from individuals aged 20 to 59. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in bisulfite converted DNA. Samples included 12 of each blood, saliva and semen samples from 18 male donors aged 20 to 59, and 3 of each vaginal fluid and menstrual blood samples from 4 female donors in their twenties. Genome-wide DNA methylation profiling of body fluids obtained from young and old individuals. The Illumina Infinium 450K Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450K CpGs from human body fluids including blood, saliva, semen, vaginal fluid and menstrual blood. Bisulfite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
2015-05-26 | E-GEOD-59505 | biostudies-arrayexpress
Project description:In this study, small RNAs were isolated from individual donations of eight forensically relevant biological fluids (blood, semen, vaginal fluid, menstrual blood, saliva, urine, feces, and perspiration) and subjected to next generation sequencing using the Illumina® Hi-Seq platform. Sequencing reads were aligned and annotated against miRbase release 21, resulting in a list of miRNAs and their relative expression levels for each sample analyzed. Body fluids with high bacterial loads (vaginal fluid, saliva, and feces) yielded relatively low annotated miRNA counts, likely due to oversaturation of small RNAs from the endogenous bacteria. Both body-fluid specific and potential normalization miRNAs were identified for further analysis as potential body fluid identification tools for each body fluid. 32 samples - 3-5 replicates of each human biological fluid: venous blood, urine, semen (normal and vasectomized), vaginal secretions, menstrual secretions, perspiration, feces, saliva
2016-08-20 | E-GEOD-85830 | biostudies-arrayexpress
Project description:The ability to predict tissue type and donor’s age from molecular profiles of crime scene samples has practical implications in forensics. In order to identify body fluid- and age-associated DNA methylation changes, genome-wide DNA methylation profiling was carried out for body fluids including blood, saliva, semen, menstrual blood, and vaginal fluid obtained from individuals aged 20 to 59. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in bisulfite converted DNA. Samples included 12 of each blood, saliva and semen samples from 18 male donors aged 20 to 59, and 3 of each vaginal fluid and menstrual blood samples from 4 female donors in their twenties.
2015-05-26 | GSE59507 | GEO
Project description:The ability to predict tissue type and donor’s age from molecular profiles of crime scene samples has practical implications in forensics. In order to identify body fluid- and age-associated DNA methylation changes, genome-wide DNA methylation profiling was carried out for body fluids including blood, saliva, semen, menstrual blood, and vaginal fluid obtained from individuals aged 20 to 59. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in bisulfite converted DNA. Samples included 12 of each blood, saliva and semen samples from 18 male donors aged 20 to 59, and 3 of each vaginal fluid and menstrual blood samples from 4 female donors in their twenties.
2015-05-26 | GSE59505 | GEO
Project description:The ability to predict tissue type and donor’s age from molecular profiles of crime scene samples has practical implications in forensics. In order to identify body fluid- and age-associated DNA methylation changes, genome-wide DNA methylation profiling was carried out for body fluids including blood, saliva, semen, menstrual blood, and vaginal fluid obtained from individuals aged 20 to 59. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in bisulfite converted DNA. Samples included 12 of each blood, saliva and semen samples from 18 male donors aged 20 to 59, and 3 of each vaginal fluid and menstrual blood samples from 4 female donors in their twenties.
2015-05-26 | GSE59508 | GEO