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| Status |
Public on Oct 14, 2015 |
| Title |
Global gene expression analysis of formalin-fixed paraffin-embedded (FFPE), furan-exposed mouse liver using two-colour Agilent microarrays |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
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.
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| Overall design |
In this experiment we examined the transcriptional response of liver tissue of female B6C3F1 mice exposed to furan for 3 weeks to 8 mg/kg bw furan (or vehicle control) and sacrificed four hours after the final exposure. Each dose group had 4 biological replicates. Samples were formalin-fixed (for 18hrs or 3wks) and paraffin embedded. There were a total of 8 samples included in the final analysis of the two-colour microarrays. We used a reference design (using pooled sample cDNA as a reference), randomized block design and SurePrint G3 Mouse GE 8x60K microarrays (Agilent).
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| Contributor(s) |
Webster AF, Williams A, Recio L, Yauk CL |
| Citation(s) |
26361796 |
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| Submission date |
Oct 30, 2014 |
| Last update date |
Feb 02, 2018 |
| Contact name |
Anna Francina Jackson |
| E-mail(s) |
francina.jackson@hc-sc.gc.ca
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| Organization name |
Health Canada
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| Department |
Environmental Health Center
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| Lab |
Dr. Carole Yauk
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| Street address |
50 Colombine Drive, Tunney's Pasture
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| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1A 0K9 |
| Country |
Canada |
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| Platforms (1) |
| GPL10787 |
Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (Probe Name version) |
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| Samples (16)
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| GSM1534303 |
Liver_Control_18hr-FFPE_sample2 [2-color array] |
| GSM1534304 |
Liver_Control_18hr-FFPE_sample3 [2-color array] |
| GSM1534305 |
Liver_Control_18hr-FFPE_sample4 [2-color array] |
| GSM1534306 |
Liver_Control_18hr-FFPE_sample6 [2-color array] |
| GSM1534307 |
Liver_8mkd-furan_18hr-FFPE_sample41 [2-color array] |
| GSM1534308 |
Liver_8mkd-furan_18hr-FFPE_sample42 [2-color array] |
| GSM1534309 |
Liver_8mkd-furan_18hr-FFPE_sample43 [2-color array] |
| GSM1534310 |
Liver_8mkd-furan_18hr-FFPE_sample44 [2-color array] |
| GSM1534311 |
Liver_Control_3wk-FFPE_sample2.1 [2-color array] |
| GSM1534312 |
Liver_Control_3wk-FFPE_sample2.2 [2-color array] |
| GSM1534313 |
Liver_Control_3wk-FFPE_sample4 [2-color array] |
| GSM1534314 |
Liver_Control_3wk-FFPE_sample6 [2-color array] |
| GSM1534315 |
Liver_8mkd-furan_3wk-FFPE_sample41 [2-color array] |
| GSM1534316 |
Liver_8mkd-furan_3wk-FFPE_sample42 [2-color array] |
| GSM1534317 |
Liver_8mkd-furan_3wk-FFPE_sample43 [2-color array] |
| GSM1534318 |
Liver_8mkd-furan_3wk-FFPE_sample44 [2-color array] |
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| This SubSeries is part of SuperSeries: |
| GSE62843 |
Global gene expression analysis in paired fresh-frozen and FFPE furan-exposed mouse liver samples |
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| Relations |
| BioProject |
PRJNA265830 |
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