Data from: Demodifying RNA for transcriptomic analyses of archival formalin-fixed paraffin-embedded samples

Wehmas LC, Wood CE, Gagne R, Williams A, Yauk C, Gosink MM, Dalmas D, Hao R, O'Lone R, Hester S

Date Published: December 1, 2017

DOI: https://doi.org/10.5061/dryad.7c4s5

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Title Table S1
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Description Taqman primer and probe sequences for RT-qPCR mRNA integrity assay targeting Actb (NM_007393.5)
Download Table_S1_triplex_RT-qPCR_primers_20170829.xlsx (10.61 Kb)
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Title Table S2
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Description FFPE RNA fragmentation duration for library preparation
Download Table_S2_Library_prep_fragmentation_times_....xlsx (12.18 Kb)
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Title Table S3
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Description RNA yield and RNA integrity numbers
Download Table_S3_RNA_and_RNA_quality_20171031_clean.xlsx (13.88 Kb)
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Title Table S4
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Description Summary of Actb RNA copies by amplicon across different preservation conditions
Download Table_S4_Actb_amplicon_summary_20170731.xlsx (14.90 Kb)
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Title Table S5
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Description RNA-sequencing quality summary for additional metrics that A) demonstrate no chemical exposure related interaction with preservation groups and B) those that do
Download Table_S5_sequencing_quality_metrics_201710....xlsx (44.09 Kb)
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Title Table S6
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Description Summary of total gene counts and quantity of unique genes identified prior to count normalization
Download Table_S6_total_and_unique_raw_gene_ct_summ....xlsx (14.45 Kb)
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Title Table S7
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Description All significant differentially expressed genes identified between preservation groups
Download Table_S7_differentially_expressed_genes_20....xlsx (140.5 Kb)
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Title Table S8
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Description Significant differentially expressed genes list from each preservation group overlapping with FR
Download Table_S8_overlapping_deg_lists_vs_fr_20171031.xlsx (116.8 Kb)
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Title Table S9
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Description TMM normalized and raw biomarker (Cyp2b10, Cyp3a11) and housekeeping gene (Gapdh) count summaries
Download Table_S9_raw_normalized_biomarker_counts_2....xlsx (19.61 Kb)
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Title Table S10
Downloaded 1 time
Description Significantly enriched canonical pathways from IPA ranked by p-value or z-score relative to FR
Download Table_S10_Canonical_pathways_ranked_201710....xlsx (233.5 Kb)
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Title Table S11
Downloaded 1 time
Description Linear regression analyses comparing –log10 of pathway p-values and upstream regulator z-scores from the frozen (FR) sample versus predictions from respective preservation procedures
Download Table_S11_Linear_regression_analysis_pathw....xlsx (9.743 Kb)
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Title Table S12
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Description Ingenuity Pathway Analysis upstream regulator comparison ranked relative to FR p-value
Download Table_S12_Upstream_regulator_rank_20171031.xlsx (82.88 Kb)
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Title Table S13
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Description Casual network analysis comparing -log10(p-values) across preservation groups
Download Table_S13_Casual_network_analysis_20171031.xlsx (36.78 Kb)
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Title Figure S1
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Description Correlation analysis by log fold change of the differentially expressed genes found within each preservation condition and corresponding frozen group. Abbreviations: FR - frozen, OH - ethanol, 18F – 18hr formalin, 3F - 3m formalin, DTAE - Demod Tris-Acetate EDTA, DQ - Demod 18hr Qiagen, DP - Demod 18hr PureLink, and NoD - Control no catalyst
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Title Figure S2
Downloaded 2 times
Description Plot of –log10 of pathway p-values from the frozen (FR) sample versus pathway predictions from the other preservation procedures. Best fit linear regression line is shown and line expression is shown in the upper right side of each panel. Panels are: A) FR versus OH; B) FR versus 18F; C) FR versus DTAE; D) FR versus DP; E) FR versus DQ; F) FR versus NoD; G) FR versus 3F. Abbreviations: FR - frozen, OH - ethanol, 18F – 18hr formalin, 3F - 3m formalin, DTAE - Demod Tris-Acetate EDTA, DQ - Demod 18hr Qiagen, DP - Demod 18hr PureLink, and NoD - Control no catalyst
Download FigS2.tif (34.72 Mb)
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Title Figure S3
Downloaded 1 time
Description Plot of Upstream Regulator activation z-scores from the frozen (FR) sample versus Upstream Regulator activation z-scores from the other isolation procedures. Best fit linear regression line is shown and line expression is shown in the upper right side of each panel. Panels are: A) FR versus DP; B) FR versus 18F; C) FR versus DTAE; D) FR versus OH; E) FR versus DQ; F) FR versus 3F; G) FR versus NoD. Abbreviations: FR - frozen, OH - ethanol, 18F – 18hr formalin, 3F - 3m formalin, DTAE - Demod Tris-Acetate EDTA, DQ - Demod 18hr Qiagen, DP - Demod 18hr PureLink, and NoD - Control no catalyst
Download FigS3.tif (34.72 Mb)
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When using this data, please cite the original publication:

Wehmas LC, Wood CE, Gagne R, Williams A, Yauk C, Gosink MM, Dalmas D, Hao R, O’Lone R, Hester S (2017) Demodifying RNA for transcriptomic analyses of archival formalin-fixed paraffin-embedded samples. Toxicological Sciences, online in advance of print. https://doi.org/10.1093/toxsci/kfx278

Additionally, please cite the Dryad data package:

Wehmas LC, Wood CE, Gagne R, Williams A, Yauk C, Gosink MM, Dalmas D, Hao R, O'Lone R, Hester S (2017) Data from: Demodifying RNA for transcriptomic analyses of archival formalin-fixed paraffin-embedded samples. Dryad Digital Repository. https://doi.org/10.5061/dryad.7c4s5
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