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| Status |
Public on Feb 28, 2018 |
| Title |
Demodifying RNA for Transcriptomic Analyses of Archival Formalin-Fixed Paraffin-Embedded Samples |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Frozen mouse liver samples from control and phenobarbital exposed groups (n=6/group) were divided and preserved for 3 months as follows: frozen (FR, high quality RNA control); 70% ethanol (OH, fixative control); 10% buffered formalin for 18 hours followed by ethanol (18F); and 10% buffered formalin (3F, demodification control). 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 (catalyst control). TruSeq Stranded Total RNA libraries with Ribo-Zero were built and sequenced using the Illumina HiSeq platform.
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| Contributor(s) |
Wehmas LC, Wood CE, Gagne R, Williams A, Yauk C, Gosink M, Dalmas D, Hao R, O'Lone R, Hester S |
| Citation(s) |
29228314 |
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| Submission date |
Sep 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Susan Hester |
| E-mail(s) |
hester.susan@epa.gov
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| Phone |
919-541-1320
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| Organization name |
US EPA
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| Street address |
109 TW Alexander Dr
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| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27711 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (96)
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| Relations |
| BioProject |
PRJNA401796 |
| SRA |
SRP116969 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE103440_normalized_count_matrix.txt.gz |
10.5 Mb |
(ftp)(http) |
TXT |
| GSE103440_raw_count_matrix.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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