Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Direct Formalin Fixation Induces Widespread Transcriptomic Effects in Archival Tissue Samples

ABSTRACT: 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. Samples were divided into: (1) fresh-frozen (FR); (2) directly fixed in 10% buffered formalin for 18 hours followed by paraffin embedding (FFPE); (3) frozen then fixed as FFPE (FR>FFPE); or (4) frozen then fixed in 70% ethanol followed by paraffin embedding (FR>OH) (n=6/group/condition). Direct fixation resulted in 2946 differentially expressed genes (DEGs), 98% of which were down-regulated. Freezing prior to fixation resulted in ≥95% fewer DEGs vs. FR, indicating that most formalin-derived transcriptional effects occurred with fixation. This was supported by follow-up studies, which identified consistent enrichment in oxidative stress, mitochondrial dysfunction, and transcription elongation pathways with formalin fixation. Notably, formalin fixation in the parent study did not significantly impact chemical response profiles, which were consistent with CAR/PXR activation and 600 ppm phenobarbital exposure. Our results demonstrate distinct transcriptional effects of formalin fixation that could impact gene expression studies using FFPE samples.

ORGANISM(S): Mus musculus Rattus norvegicus

PROVIDER: GSE148174 | GEO | 2020/09/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Project description: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). Samples from OH, 18F, and 3F groups were processed to FFPE blocks and sectioned for RNA isolation. The latter group received no additional treatment (3F) or the following demodification protocols: short heated incubation with TAE buffer; overnight heated incubation with an organocatalyst using two different isolation kits; or overnight heated incubation without organocatalyst. TruSeq Stranded Total RNA libraries with Ribo-Zero were built and sequenced using the Illumina HiSeq platform. Extended incubation with or without organocatalyst increased RNA yield >3-fold and enhanced quality compared to 3F, as indicated by higher RNA integrity number (>1.5-fold) and fragment analysis values (>3.0-fold). Post-sequencing metrics showed reduced bias in gene coverage and deletion rates for all extended incubation groups. Following PB-induced differential gene expression analysis, all demodification groups showed increased overlap with FR in genes (73-83%) and pathways (91-94%) compared to 3F overlap with FR (60% and 63%, respectively). These results demonstrate simple changes in RNA isolation methods that can enhance genomic analyses of FFPE samples.

2018-02-28 | GSE103440 | GEO

Expanding epigenomics to archived FFPE tissues: An evaluation of DNA repair methodologies

2014-12-17 | GSE59038 | GEO

An array based analysis of miRNA expression comparing matched frozen and FFPE human tissue samples

Project description:MicroRNAs (miRNAs) are small non-coding RNAs that repress gene expression at the post transcriptional level via an antisense RNA-RNA interaction. Generally, miRNAs derived from snap frozen or fresh samples are used for array based profiling. Since tissues in most pathology departments are available only in formalin fixed and paraffin embedded state, we sought to evaluate the miRNA derived from formalin fixed and paraffin embedded (FFPE) samples for microarray analysis. In this study, miRNAs extracted from matched snap frozen and FFPE samples were profiled using the Agilent miRNA array platform. Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. A total of seven cases were compared in either duplicate or triplicate. Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results, as technical replicates showed high correlations (Kendall tau=0.722-0.853, Spearman rank correlation coefficient=0.891-0.954). Our results showed consistent high correlation between matched frozen and FFPE samples (Kendall tau=0.669-0.815, Spearman rank correlation coefficient=0.847-0.948), supporting the use of FFPE-derived miRNAs for profiling. Keywords: formalin-fixed and paraffin-embedded (FFPE) miRNA profiling

2008-11-01 | GSE12458 | GEO

Expanding epigenomics to archived FFPE tissues: An evaluation of DNA repair methodologies

Project description:A study to evaluate techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissue samples by direct comparison of FFPE DNA repair methods prior to analysis on genome-wide methylation array to matched fresh frozen (FF) tissues. Formalin-fixed paraffin-embedded tissue from three colon adenocarcinoma samples were subjected to different FFPE-oriented DNA repair approaches and sequences, then compared with corresponding fresh frozen tissues. All samples were hybridized to the Illumina Infinium 450k Human Methylation BeadChip.

2014-12-17 | E-GEOD-59038 | biostudies-arrayexpress

The microRNA profiles of ovarian clear cell carcinoma

Project description:To investigate the microRNA profiles of ovarian clear cell carcinoma (OCCC), microRNA sequencing was performed using formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen clinical samples. Moreover, patient-derived xenograft (PDX) tumors and cell lines were also investigated.

2022-04-16 | GSE200852 | GEO

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

Project description: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.

2015-10-14 | GSE62842 | GEO

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

Project description: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.

2015-10-14 | GSE62840 | GEO

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

Project description: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. All samples (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using one-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles.

2015-10-14 | GSE62838 | GEO

Project description:Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients

2016-11-30 | GSE90463 | GEO

Project description:Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients

2016-11-30 | GSE89193 | GEO