Similar studies for GEO DataSets (Select 200062843) - GEO DataSets

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Items: 20

Select item 2000628431.

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 2000643712.

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

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Select item 2000643703.

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

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Select item 2000628424.

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 2000628405.

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 2000628386.

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 2000789627.

Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples

(Submitter supplied) Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-seq offers a novel way to address this problem. In this study we evaluated transcriptomic dose responses using RNA-seq in paired FFPE and frozen (FROZ) samples from two archival studies in mice, one recent (<2 years old) and the other older (>20 years old). more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
80 Samples

Download data: TXT

Series

Accession:: GSE78962

ID:: 200078962

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Select item 2000409908.

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 2001034409.

Demodifying RNA for Transcriptomic Analyses of Archival Formalin-Fixed Paraffin-Embedded Samples

(Submitter supplied) Low RNA yield and quality limit use of formalin-fixed paraffin-embedded (FFPE) tissue samples for genomic analyses. In this study, we evaluated methods to demodify RNA highly fragmented and crosslinked by formalin fixation. Primary endpoints were RNA recovery, RNA-sequencing quality metrics, and target gene responses to a reference chemical (phenobarbital, PB). Frozen mouse liver samples from control and PB groups (n=6/group) were divided and preserved for 3 months as follows: frozen (FR); 70% ethanol (OH); 10% buffered formalin for 18 hours followed by ethanol (18F); and 10% buffered formalin (3F). more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
96 Samples

Download data: TXT

Series

Accession:: GSE103440

ID:: 200103440

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Select item 20005178310.

Comparison of Poly(A) capture versus Ribosomal RNA depletion methods for RNA-seq

(Submitter supplied) Methods: RNA-sequencing was performed on matched samples obtained across several different gene expression measurement methods including: (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN. We also assayed the matched samples with Agilent microarray. RNA-seq data was compared on the rRNA-removal efficiency, genome profile, library complexity, coverage uniformity and quantitative cosinstency across protocols and with microarray data. more...

Organism:: Homo sapiens

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

Platforms:: GPL8269 GPL11154
59 Samples

Download data: TXT

Series

Accession:: GSE51783

ID:: 200051783

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Select item 20014817411.

Direct Formalin Fixation Induces Widespread Transcriptomic Effects in Archival Tissue Samples

(Submitter supplied) Archival formalin-fixed paraffin-embedded (FFPE) tissue samples hold a wealth of transcriptomic information; however, little is known about potential artifacts. Previously, we identified a consistent shift in global RNA-sequencing profiles between matching frozen and FFPE samples. We hypothesized that this shift was from fixing fresh tissue in formalin. To test this idea, RNA-sequencing was performed on liver samples collected from male mice treated with 600 ppm of a reference chemical (phenobarbital, 600 ppm phenobarbital) or vehicle control for 7 days. more...

Organism:: Mus musculus; Rattus norvegicus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL25029 GPL21626 GPL17021
96 Samples

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Series

Accession:: GSE148174

ID:: 200148174

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Select item 20011397612.

mRNA-seq Whole Transcriptome Profiling of Fresh Frozen versus Archived Fixed Tissues

(Submitter supplied) Background: The main bottleneck for genomic studies of tumors is the limited availability of fresh frozen (FF) samples collected from patients, coupled with comprehensive long-term clinical follow-up. This shortage could be alleviated by using existing large archives of routinely obtained and stored Formalin-Fixed Paraffin-Embedded (FFPE) tissues. However, since these samples are partially degraded, their RNA sequencing is technically challenging. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
23 Samples

Download data: TXT

Series

Accession:: GSE113976

ID:: 200113976

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Select item 20010463413.

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 20010456814.

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 20010456215.

Systematic evaluation of RNA quality and microarray data reliability in human 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:: 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 20010456116.

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

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 20008371717.

Identification and validation of differentially expressed transcripts by RNA-Sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis

(Submitter supplied) BACKGROUND: Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A major limitation in transcriptomic profiling of lung tissue in IPF has been a dependence on snap-frozen fresh tissues (FF). In this project we sought to determine whether RNA-Seq could be used to identify IPF expression profiles from archived Formalin-Fixed Paraffin-Embedded (FFPE) lung fibrotic tissue. RESULTS: We isolated total RNA from 7 IPF and 5 control FFPE lung tissues (median archived time 6 years) and performed 50 bp paired-end sequencing on Illumina 2000 HiSeq. more...