GEO DataSets

(Submitter supplied) Assay performance with low RNA inputs

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

32 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

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

164 Samples

Download data

(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 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) Background: To date, few studies have systematically characterized microarray gene expression signal performance with degraded RNA from formalin-fixed paraffin-embedded (FFPE) specimens in comparison to intact RNA from unfixed fresh-frozen (FF) specimens. Methodology: RNA was extracted and isolated from paired tumor and normal samples from both FFPE and FF kidney, lung and colon tissue specimens. Microarray signal dynamics on both the raw probe and probeset level were evaluated. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL571 GPL570

53 Samples

Download data: CEL

(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) 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) 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

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

Organism:

Homo sapiens; Rattus norvegicus

Type:

Expression profiling by array

Platforms:

GPL17117 GPL16686

15 Samples

Download data: CEL

(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