GEO DataSets

(Submitter supplied) The Formalin-Fixed Paraffin-Embedded (FFPE) samples on selected breast cancer subtypes (ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2-) and their paired fresh fine needle aspirated biopsies (FNA) were investigated. The cases represented different subtypes of breast cancers based on their clinical receptors ER (E) and Her2 (H) status to demonstrate the ability of gene profiles to differentiate these tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

25 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL8432 GPL6883

50 Samples

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(Submitter supplied) The Formalin-Fixed Paraffin-Embedded (FFPE) samples on selected breast cancer subtypes (ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2-) and their paired fresh fine needle aspirated biopsies (FNA) were investigated. The cases represented different subtypes of breast cancers based on their clinical receptors ER (E) and Her2 (H) status to demonstrate the ability of gene profiles to differentiate these tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8432

25 Samples

Download data: TXT

(Submitter supplied) Analysis of 97 formalin-fixed, paraffin-embedded (FFPE) primary breast tumors using Illumina DASL microarray technology on a Custom Breast Cancer Panel and the Illumina Human Cancer Panel. Molecular markers between the pathology defined subtypes of breast cancer were assessed to hypothesize potential therapeutic targets specific to the subtypes

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL9006 GPL5858

177 Samples

Download data: TXT

(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

(Submitter supplied) Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin fixed paraffin embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumor banks. Once samples are fixed in formalin the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study we have evaluated the whole genome DASL assay from Illumina to perform transcriptomic analysis from archived breast tumor tissue fixed in formalin paraffin embedded blocks. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8432

85 Samples

Download data: TXT

(Submitter supplied) Archival Formalin-Fixed Paraffin Embedded (FFPE) tissue represents an abundant and more easily transferable source of patient tissue than live specimens. Furthermore cancer FFPE tissue deposited at major cancer research institutes is often paired with survival data increasing the value of biomarker and prediction based research from these samples. However the known fragility of RNA and artifacts introduced through the processes of tissue preservation and storage introduce the possibility of unfaithful RNA expression signatures from these sources. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

21 Samples

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(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:

GPL13112 GPL10787

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

24 Samples

Download data: TXT

(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

Download data: TXT

(Submitter supplied) Assay performance with mixed RNA samples

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

18 Samples

Download data: TXT

(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

Download data: TXT