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A method of stripping custom microarrays

ABSTRACT: Our genome wide analyses of microRNA expression profiles involve the hybridization of fluorescently labeled RNA samples to custom made, DNA microarrays based on the GAPSII coated slides. We describe a simple and effective method to regenerate such custom microarrays. Our protocol entails the use of a very low concentration of sodium hydroxide in a low salt buffer to strip RNA molecules from the arrays. The solution is also capable of removing DNA molecules hybridized to the slides, while preserving the slide coating and printed DNA probes. Slides can be stripped and reused at least twice without significantly sacrificing data quality. Keywords: expression study, new vs. stripped array comparison

ORGANISM(S): Rattus norvegicus Mus musculus synthetic construct Danio rerio Homo sapiens Caenorhabditis elegans Drosophila melanogaster

PROVIDER: GSE10305 | GEO | 2008/10/01

SECONDARY ACCESSION(S): PRJNA108525

REPOSITORIES: GEO

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A method of stripping custom microarrays

Project description:Our genome wide analyses of microRNA expression profiles involve the hybridization of fluorescently labeled RNA samples to custom made, DNA microarrays based on the GAPSII coated slides. We describe a simple and effective method to regenerate such custom microarrays. Our protocol entails the use of a very low concentration of sodium hydroxide in a low salt buffer to strip RNA molecules from the arrays. The solution is also capable of removing DNA molecules hybridized to the slides, while preserving the slide coating and printed DNA probes. Slides can be stripped and reused at least twice without significantly sacrificing data quality. Keywords: expression study, new vs. stripped array comparison There are two stripping conditions in this study (1mM NaOH and 2mM NaOH in SSC buffer). For 1mM NaOH treatment, new, once-, twice-, and triple-stripped arrays are studies. For 2mM NaOH treatment, new and once-stripped arrays are measured.

2010-05-19 | E-GEOD-10305 | biostudies-arrayexpress

High Reproducibility Using Sodium Hydroxide Stripped Long Oligonucleotide DNA Microarrays

Project description:Recently, long oligonucleotide (60-70mer) microarrays for two-color experiments have been developed and are gaining widespread use. In addition, when there is limited availability of mRNA from tissue sources, RNA amplification can and is being used to produce sufficient quantities of cRNA for microarray hybridization. Taking advantage of the selective degradation of RNA under alkaline conditions, we have developed a method to “strip” glass-based oligonucleotide microarrays that use fluorescent RNA in the hybridization, while leaving the DNA oligonucleotide probes intact and usable for a second experiment. Replicate microarray experiments conducted using stripped arrays showed high reproducibility, however, we found that arrays could only be stripped and reused once without compromising data quality. The intraclass correlation (ICC) between a virgin array and a stripped array hybridized with the same sample showed a range of 0.90-0.98, which is comparable to the ICC of two virgin arrays hybridized with the same sample. Using this method, once stripped oligonucleotide microarrays are usable, reliable, and should help to reduce costs. Keywords = Agilent microarray Keywords = Stripped arrays Keywords = Replicate reproducibility Keywords: other

2005-02-23 | GSE1706 | GEO

Homo sapiens

Project description:High Reproducibility Using Sodium Hydroxide Stripped Long Oligonucleotide DNA Microarrays

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The proteome of hand eczema assessed by tape stripping

Project description:Hand eczema (HE) is a prevalent skin disease. However, classification of HE into different subtypes remains challenging. Limited number of prior studies have employed invasive biopsy-based strategies; yet, studies of the HE proteome using non-invasive tape stripping methodology have not been reported. In this study, we wanted to assess whether global proteomic analysis of skin tape strip samples can be used for sub-classification of HE patients. Tape strips were collected from patients with HE and healthy skin. Liquid chromatography–mass spectrometry (LC/MS) proteomics was performed, and the global protein expression was analyzed. We identified 2,919 proteins in stratum corneum-derived skin cells from tape strip samples. Compared to healthy skin, the lesional samples from HE patients exhibited increased expression of immune-related markers and a decreased expression of structural barrier proteins. The difference between HE subtypes was restricted to the lesional skin areas, and included an increased expression of skin barrier-related proteins independently of the concurrent AD. In conclusion we found, that the non-invasive tape strip method used in combination with LC/MS proteomics can be used for analysis of skin protein expression in HE patients. Thus, the method shows potential for assessing the proteomic differences between subtypes of HE, and biomarker discovery.

2023-04-26 | PXD039665 | Pride

High Reproducibility Using Sodium Hydroxide Stripped Long Oligonucleotide DNA Microarrays

Project description:Recently, long oligonucleotide (60-70mer) microarrays for two-color experiments have been developed and are gaining widespread use. In addition, when there is limited availability of mRNA from tissue sources, RNA amplification can and is being used to produce sufficient quantities of cRNA for microarray hybridization. Taking advantage of the selective degradation of RNA under alkaline conditions, we have developed a method to â??stripâ?? glass-based oligonucleotide microarrays that use fluorescent RNA in the hybridization, while leaving the DNA oligonucleotide probes intact and usable for a second experiment. Replicate microarray experiments conducted using stripped arrays showed high reproducibility, however, we found that arrays could only be stripped and reused once without compromising data quality. The intraclass correlation (ICC) between a virgin array and a stripped array hybridized with the same sample showed a range of 0.90-0.98, which is comparable to the ICC of two virgin arrays hybridized with the same sample. Using this method, once stripped oligonucleotide microarrays are usable, reliable, and should help to reduce costs. Keywords = Agilent microarray Keywords = Stripped arrays Keywords = Replicate reproducibility Keywords: other

2010-06-10 | E-GEOD-1706 | biostudies-arrayexpress

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Project description:new and stripped microarrays Keywords: reuse of Agilent custom 8.4 in situ microarrays

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The stratum corneum transcriptome in atopic dermatitis can be assessed by tape stripping

Project description:Background: Skin biopsies represent a gold standard in skin immunology and pathology but can cause pain and induce scarring. Non-invasive techniques will facilitate study recruitment of e.g. patients with pediatric atopic dermatitis (AD), hand eczema or facial dermatitis. Objective: By RNA sequencing, we examined whether the stratum corneum transcriptome in AD skin can be assessed by tape stripping, as compared to the epidermal transcriptome of AD in skin biopsies. To make the procedure clinically relevant tape strips were stored and shipped at room temperature for up to 3 days. Methods: Nine adult Caucasian AD patients and three healthy volunteers were included. Tape samples were collected from non-lesional and lesional skin. Biopsies were collected from lesional skin and were split into epidermis and dermis. Total RNA was extracted, and shotgun sequencing was performed. Results: Shotgun sequencing could be performed on skin cells obtained from two consecutive tape strips which had been stored and shipped at room temperature for up to three days. The most prominent differences between the tape strip and biopsy derived transcriptome were due to structural genes, while established molecular markers of AD, including CCL17, CCL22, IL17A and S100A7-S100A9, were also identified in tape strip samples. Furthermore, the tape strip derived transcriptome showed promise in also analysing the skin microbiome. Conclusion: Our study shows that the stratum corneum (SC) transcriptome of AD can be assessed by tape stripping the skin, supporting that this method may be central in future skin biomarker research.

2020-10-31 | GSE160501 | GEO

A method of stripping custom microarrays

Project description:A method of stripping custom microarrays

| PRJNA108525 | ENA

Profilig the Atopic Dermatitis Epidermal Transcriptome by Tape Stripping and BRB-seq

Project description:Tape stripping has recently gained use for the study of the transcriptome of atopic dermatitis (AD), a common inflammatory skin disorder characterized by a defective epidermal barrier and perturbated immune response. Here, we performed BRB-seq (a low cost, multiplex-based, transcriptomic profiling technique) to study the epidermal transcriptome of AD patients and healthy controls from tape stripped skin samples.

2022-05-31 | GSE199046 | GEO

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Project description:Our analyses of microRNA expression profiles involve the hybridization of fluorescently labeled miRNA samples to custom made, DNA microarrays based on the GAPSII coated slides. We hybridized different amounts of microRNAs from the mirVana miRNA Reference Panel v9.1 to microarrays. Keywords: Expression

2009-07-30 | GSE11176 | GEO

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