Similar studies for GEO DataSets (Select 200104561) - GEO DataSets

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Items: 20

Select item 2001045611.

Systematic evaluation of RNA quality and microarray data reliability in rat formalin-fixed paraffin-embedded and fresh frozen tissue samples

(Submitter supplied) We assessed the feasibility and reliability of microarray studies using formalin-fixed paraffin-embedded (FFPE) tissue-derived RNA compared with transcriptome data from paired fresh-frozen (FF) material. We established a robust workflow to generate highly reproducible microarray datasets from only 2 ng RNA input. For prior quality assessment, inspection of Agilent Bioanalyzer electropherograms, calculation of RNA fragment size distribution (DV200) and routine qPCR for selected references genes were done.

Organism:: Rattus norvegicus

Type:: Expression profiling by array

Platform:: GPL17117
6 Samples

Download data: CEL, TXT

Series

Accession:: GSE104561

ID:: 200104561

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Select item 2001046342.

Analysis of microarray data reliability and pathway networks using experimental formalin-fixed paraffin-embedded tissue

(Submitter supplied) We assessed the usability of microarrays, which base on formalin-fixed paraffin-embedded (FFPE) tissue.

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL17400
16 Samples

Download data: CEL

Series

Accession:: GSE104634

ID:: 200104634

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Select item 2001045683.

Systematic evaluation of RNA quality and microarray data reliability in formalin-fixed paraffin-embedded and fresh frozen tissue samples

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Rattus norvegicus; Homo sapiens

Type:: Expression profiling by array

Platforms:: GPL17117 GPL16686
15 Samples

Download data: CEL

Series

Accession:: GSE104568

ID:: 200104568

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Select item 2001045624.

Systematic evaluation of RNA quality and microarray data reliability in human formalin-fixed paraffin-embedded and fresh frozen tissue samples

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL16686
9 Samples

Download data: CEL, TXT

Series

Accession:: GSE104562

ID:: 200104562

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Select item 2000409905.

Preparation of archival formalin-fixed paraffin-embedded mouse liver samples for use with the Agilent gene expression microarray platform

(Submitter supplied) For decades, formalin-fixing and paraffin embedding (FFPE) has been routinely used to preserve tissue samples for histological analysis. Global gene expression analysis of these archival tissues has the potential to greatly advance research attempting to link perturbations in molecular pathways to disease outcome. We investigated 16-year-old FFPE mouse liver samples treated with phenobarbital and created a protocol for their analysis using Agilent gene expression arrays. more...

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL13912
28 Samples

Download data: TXT

Series

Accession:: GSE40990

ID:: 200040990

Select item 2000643716.

Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using RNA-seq [polyA enrichment]

(Submitter supplied) Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using RNA-seq (polyA-enrichment protocol). All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using one- and two-colour microarrays and RNA-seq (ribo-depletion protocol) in order to determine the effect of the technology on gene expression profiles.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13112
24 Samples

Download data: TXT

Series

Accession:: GSE64371

ID:: 200064371

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000643707.

Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using RNA-seq [ribo-depletion]

(Submitter supplied) Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using RNA-seq (ribo-depletion protocol). All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using one- and two-colour microarrays and RNA-seq (polyA-enrichment protocol) in order to determine the effect of the technology on gene expression profiles.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13112
24 Samples

Download data: TXT

Series

Accession:: GSE64370

ID:: 200064370

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000628438.

Global gene expression analysis in paired fresh-frozen and FFPE furan-exposed mouse liver samples

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Mus musculus

Type:: Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:: GPL13112 GPL10787
122 Samples

Download data: TXT, XLSX

Series

Accession:: GSE62843

ID:: 200062843

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Select item 2000628429.

Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using one-colour Agilent microarrays

(Submitter supplied) Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using one-colour microarrays. All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using two-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles.

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL10787
8 Samples

Download data: TXT

Series

Accession:: GSE62842

ID:: 200062842

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Select item 20006284010.

Global gene expression analysis of formalin-fixed paraffin-embedded (FFPE), furan-exposed mouse liver using one-colour Agilent microarrays

(Submitter supplied) Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using one-colour microarrays. To determine the effect of time-in-formalin on gene expression signatures we performed microarray analysis of livers that were fixed in formalin for 18 hours or 3 weeks. All samples (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using two-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles.

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL10787
50 Samples

Download data: TXT

Series

Accession:: GSE62840

ID:: 200062840

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Select item 20006283811.

Global gene expression analysis of formalin-fixed paraffin-embedded (FFPE), furan-exposed mouse liver using two-colour Agilent microarrays

(Submitter supplied) Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen (GSE48644) and formalin-fixed paraffin embedded (FFPE; this study) samples using two-colour microarrays. To determine the effect of time-in-formalin on gene expression signatures we performed microarray analysis of livers that were fixed in formalin for 18 hours or 3 weeks. more...

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL10787
16 Samples

Download data: TXT

Series

Accession:: GSE62838

ID:: 200062838

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Select item 20017350612.

Application of the 3’ mRNA-Seq using unique molecular identifiers in highly degraded RNA derived from formalin-fixed, paraffin-embedded tissue

(Submitter supplied) Background: Archival formalin-fixed, paraffin-embedded (FFPE) tissue samples with clinical and histological data are a singularly valuable resource for developing new molecular biomarkers. However, transcriptome analysis remains challenging with standard mRNA-seq methods as FFPE derived-RNA samples are often highly modified and fragmented. The recently developed 3’ mRNA-seq method sequences the 3’ region of mRNA using unique molecular identifiers (UMI), thus generating gene expression data free from PCR amplification bias. more...