GEO DataSets

(Submitter supplied) Background and Aims Formalin-fixed, paraffin-embedded (FFPE) tissue is the most commonly available form of archived clinical specimens, which are often stored as thin sections on glass slides. RNA isolated from such archived section (AS) of FFPE tissue is more degraded compared to freshly cut (FC) FFPE section because of prolonged air exposure. In this study, we evaluated performance of transcriptome profiling-based disease classification in AS-FFPE tissue. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13369

136 Samples

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL17230 GPL13369

160 Samples

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(Submitter supplied) Background and Aims Formalin-fixed, paraffin-embedded (FFPE) tissue is the most commonly available form of archived clinical specimens, which are often stored as thin sections on glass slides. RNA isolated from such archived section (AS) of FFPE tissue is more degraded compared to freshly cut (FC) FFPE section because of prolonged air exposure. In this study, we evaluated performance of transcriptome profiling-based disease classification in AS-FFPE tissue. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17230

24 Samples

Download data: TXT

(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

(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

(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:

GPL10787 GPL13112

122 Samples

Download data: TXT, XLSX

(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

(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

(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

(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

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(Submitter supplied) Performance assayed with formalin-fixed, paraffin-embedded (FFPE) ovarian tumor tissues.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

24 Samples

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(Submitter supplied) Performance assayed with formalin-fixed, paraffin-embedded (FFPE) ovarian tumor tissues.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

42 Samples

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

164 Samples

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(Submitter supplied) Cross-platform comparison between WG-DASL and IVT-based assays

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

8 Samples

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(Submitter supplied) Assay performance with mixed RNA samples

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

18 Samples

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(Submitter supplied) Performance assayed with FFPE tissues

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

16 Samples

Download data: TXT

(Submitter supplied) Assay performance with low RNA inputs

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

32 Samples

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(Submitter supplied) Assay performance comparison between intact and artificially degraded RNA samples

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

8 Samples

Download data: TXT

(Submitter supplied) Comparison between fresh-frozen and Formalin-Fixed, Paraffin-Embedded tissues

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

16 Samples

Download data: TXT

(Submitter supplied) To study feasibility of gene expression profiling from FFPE tissues using NanoString nCounter platform, we designed a pilot study utilizing samples from ovarian cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18292

24 Samples

Download data: TXT