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| Status |
Public on Oct 14, 2015 |
| Title |
Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using RNA-seq [polyA enrichment] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| 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 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.
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| Overall design |
In this study we examined the transcriptional response in 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. There were a total of 24 samples included in the final analysis of the polyA enrichment RNA-seq experiment.
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| |
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| Contributor(s) |
Webster AF, Zumbo P, Gandara J, Recio L, Yauk CL, Mason C |
| Citation(s) |
26361796 |
| |
| Submission date |
Dec 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Anna Francina Jackson |
| E-mail(s) |
francina.jackson@hc-sc.gc.ca
|
| Organization name |
Health Canada
|
| Department |
Environmental Health Center
|
| Lab |
Dr. Carole Yauk
|
| Street address |
50 Colombine Drive, Tunney's Pasture
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1A 0K9 |
| Country |
Canada |
| |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (24)
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| GSM1569662 |
Liver_Control_FFPE18h_06_polyA-RNAseq |
| GSM1569663 |
Liver_8mkd-furan_FFPE18h_41_polyA-RNAseq |
| GSM1569664 |
Liver_8mkd-furan_FFPE18h_42_polyA-RNAseq |
| GSM1569665 |
Liver_8mkd-furan_FFPE18h_43_polyA-RNAseq |
| GSM1569666 |
Liver_8mkd-furan_FFPE18h_44_polyA-RNAseq |
| GSM1569667 |
Liver_Control_FFPE3wk_02_polyA-RNAseq |
| GSM1569668 |
Liver_Control_FFPE3wk_03_polyA-RNAseq |
| GSM1569669 |
Liver_Control_FFPE3wk_04_polyA-RNAseq |
| GSM1569670 |
Liver_Control_FFPE3wk_06_polyA-RNAseq |
| GSM1569671 |
Liver_8mkd-furan_FFPE3wk_41_polyA-RNAseq |
| GSM1569672 |
Liver_8mkd-furan_FFPE3wk_42_polyA-RNAseq |
| GSM1569673 |
Liver_8mkd-furan_FFPE3wk_43_polyA-RNAseq |
| GSM1569674 |
Liver_8mkd-furan_FFPE3wk_44_polyA-RNAseq |
| GSM1569675 |
Liver_Control_FreshFrozen_02_polyA-RNAseq |
| GSM1569676 |
Liver_Control_FreshFrozen_03_polyA-RNAseq |
| GSM1569677 |
Liver_Control_FreshFrozen_04_polyA-RNAseq |
| GSM1569678 |
Liver_Control_FreshFrozen_06_polyA-RNAseq |
| GSM1569679 |
Liver_8mkd-furan_FreshFrozen_41_polyA-RNAseq |
| GSM1569680 |
Liver_8mkd-furan_FreshFrozen_42_polyA-RNAseq |
| GSM1569681 |
Liver_8mkd-furan_FreshFrozen_43_polyA-RNAseq |
| GSM1569682 |
Liver_8mkd-furan_FreshFrozen_44_polyA-RNAseq |
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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 |
PRJNA270847 |
| SRA |
SRP051384 |
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