Validating reference genes within a mouse model system of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity
BACKGROUND: Quantitative real-time PCR (qPCR) is the “gold-standard” technique for measuring mRNA abundances. To correctly compare samples and generate biologically valid results, qPCR data usually require comprehensive normalization to account for sample content variation between reactions. The mos...
Saved in:
Published in | Chemico-biological interactions Vol. 205; no. 1; pp. 63 - 71 |
---|---|
Main Authors | , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
Ireland
Elsevier Ireland Ltd
05.09.2013
|
Subjects | |
Online Access | Get full text |
Cover
Loading…
Abstract | BACKGROUND: Quantitative real-time PCR (qPCR) is the “gold-standard” technique for measuring mRNA abundances. To correctly compare samples and generate biologically valid results, qPCR data usually require comprehensive normalization to account for sample content variation between reactions. The most common normalization approaches use one or more endogenous controls (reference or house-keeping genes) to adjust the measured levels of experimental genes appropriately. Ideal reference genes are those that display minimal variation across experimental conditions, and thus can vary widely across different biological systems. In particular, toxicogenomic studies of transcriptionally-disruptive toxins, like 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), require careful consideration of reference genes. RESULTS: We examined seven candidate reference genes in 199 mice varying in genotype and time/dose of TCDD exposure. We assessed gene-stability in four ways: (1) the variance of the raw Cq values across biological replicates, (2) the fold-change from basal mRNA levels following treatment, (3) the inter- and intra-group stability evaluated using the NormFinder algorithm, (4) the comparative ΔCq method for each candidate gene. Univariate analyses showed Hprt and Eef1a1 are the two most stable individual reference genes. It has been suggested that using multiple genes would produce a more consistent normalization factor; multivariate analysis was performed using NormFinder. In general, stability increased with the number of genes used, but specific gene-combinations synergized. CONCLUSIONS: We have validated seven reference genes for use in analyzing mRNA abundances in mouse models of TCDD toxicity. The use of multiple reference genes increases stability, providing more consistent normalization and more reliable results. The number of reference genes used should be maximized, based on experimental capabilities (platform, sample availability, etc.). Our results show the benefit of validating reference genes using multiple methods prior to generating large biological datasets. |
---|---|
AbstractList | Background: Quantitative real-time PCR (qPCR) is the agold-standarda technique for measuring mRNA abundances. To correctly compare samples and generate biologically valid results, qPCR data usually require comprehensive normalization to account for sample content variation between reactions. The most common normalization approaches use one or more endogenous controls (reference or house-keeping genes) to adjust the measured levels of experimental genes appropriately. Ideal reference genes are those that display minimal variation across experimental conditions, and thus can vary widely across different biological systems. In particular, toxicogenomic studies of transcriptionally-disruptive toxins, like 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), require careful consideration of reference genes. BACKGROUND: Quantitative real-time PCR (qPCR) is the “gold-standard” technique for measuring mRNA abundances. To correctly compare samples and generate biologically valid results, qPCR data usually require comprehensive normalization to account for sample content variation between reactions. The most common normalization approaches use one or more endogenous controls (reference or house-keeping genes) to adjust the measured levels of experimental genes appropriately. Ideal reference genes are those that display minimal variation across experimental conditions, and thus can vary widely across different biological systems. In particular, toxicogenomic studies of transcriptionally-disruptive toxins, like 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), require careful consideration of reference genes. RESULTS: We examined seven candidate reference genes in 199 mice varying in genotype and time/dose of TCDD exposure. We assessed gene-stability in four ways: (1) the variance of the raw Cq values across biological replicates, (2) the fold-change from basal mRNA levels following treatment, (3) the inter- and intra-group stability evaluated using the NormFinder algorithm, (4) the comparative ΔCq method for each candidate gene. Univariate analyses showed Hprt and Eef1a1 are the two most stable individual reference genes. It has been suggested that using multiple genes would produce a more consistent normalization factor; multivariate analysis was performed using NormFinder. In general, stability increased with the number of genes used, but specific gene-combinations synergized. CONCLUSIONS: We have validated seven reference genes for use in analyzing mRNA abundances in mouse models of TCDD toxicity. The use of multiple reference genes increases stability, providing more consistent normalization and more reliable results. The number of reference genes used should be maximized, based on experimental capabilities (platform, sample availability, etc.). Our results show the benefit of validating reference genes using multiple methods prior to generating large biological datasets. Quantitative real-time PCR (qPCR) is the "gold-standard" technique for measuring mRNA abundances. To correctly compare samples and generate biologically valid results, qPCR data usually require comprehensive normalization to account for sample content variation between reactions. The most common normalization approaches use one or more endogenous controls (reference or house-keeping genes) to adjust the measured levels of experimental genes appropriately. Ideal reference genes are those that display minimal variation across experimental conditions, and thus can vary widely across different biological systems. In particular, toxicogenomic studies of transcriptionally-disruptive toxins, like 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), require careful consideration of reference genes. We examined seven candidate reference genes in 199 mice varying in genotype and time/dose of TCDD exposure. We assessed gene-stability in four ways: (1) the variance of the raw Cq values across biological replicates, (2) the fold-change from basal mRNA levels following treatment, (3) the inter- and intra-group stability evaluated using the NormFinder algorithm, (4) the comparative ΔCq method for each candidate gene. Univariate analyses showed Hprt and Eef1a1 are the two most stable individual reference genes. It has been suggested that using multiple genes would produce a more consistent normalization factor; multivariate analysis was performed using NormFinder. In general, stability increased with the number of genes used, but specific gene-combinations synergized. We have validated seven reference genes for use in analyzing mRNA abundances in mouse models of TCDD toxicity. The use of multiple reference genes increases stability, providing more consistent normalization and more reliable results. The number of reference genes used should be maximized, based on experimental capabilities (platform, sample availability, etc.). Our results show the benefit of validating reference genes using multiple methods prior to generating large biological datasets. |
Author | Mak, Denise Y.F Petronis, Arturas Prokopec, Stephenie D Watson, John D Fox, Natalie S Chong, Lauren C Buchner, Nicholas B Pohjanvirta, Raimo Boutros, Paul C |
Author_xml | – sequence: 1 fullname: Prokopec, Stephenie D – sequence: 2 fullname: Buchner, Nicholas B – sequence: 3 fullname: Fox, Natalie S – sequence: 4 fullname: Chong, Lauren C – sequence: 5 fullname: Mak, Denise Y.F – sequence: 6 fullname: Watson, John D – sequence: 7 fullname: Petronis, Arturas – sequence: 8 fullname: Pohjanvirta, Raimo – sequence: 9 fullname: Boutros, Paul C |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23791969$$D View this record in MEDLINE/PubMed |
BookMark | eNo9kU9PGzEQxa0KVALtB-il-Eil7NZ_svb6iEJbkJA4FHq1vPZscLS7DrYjCJ8eR6FcZvSk9540vzlFR1OYAKFvlNSUUPFzXdvO14xQXhNRE9J-QjPaSlZJ2YojNCOEqIpJJU_QaUrrIglbkM_ohHGpqBJqhsZ_ZvDOZD-tcIQeIkwW8AomSPjZ50c_YYPHsE1QpoMBp13KMOLQYzbnczlvqww5Gvs4hBic72B6DdWmcj68lOzF_fLq6gfORVifd1_QcW-GBF_f9xl6-P3rfnld3d79uVle3lZ2QWiuFJPGWMs7ySwT1jiwwrWmoZ3qlJNdz5ywqnVGKdJYIcAQ0tEFE5QrruiCn6GLQ-8mhqctpKxHnywMg5mg3KJpQxlnVDR7Kz1YbQwpFQR6E_1o4k5ToveU9VoXynpPWROhC-WS-f5ev-1GcB-J_1iL4fxg6E3QZhV90g9_S0NTPiBayVv-BiXvg9c |
CitedBy_id | crossref_primary_10_20473__v8i1_19991 crossref_primary_10_3390_ijms242216277 crossref_primary_10_1371_journal_pone_0110730 crossref_primary_10_1590_S0102_865020160080000009 crossref_primary_10_3945_jn_114_195081 crossref_primary_10_1186_s12864_015_1840_6 crossref_primary_10_1186_s12864_016_3446_z crossref_primary_10_1016_j_taap_2015_02_012 |
Cites_doi | 10.1097/00001648-200001000-00010 10.1016/j.taap.2012.04.032 10.1261/rna.034710.112 10.1021/tx015589+ 10.1016/j.envres.2005.12.003 10.1006/bbrc.1995.1951 10.1016/j.cbi.2006.01.001 10.1007/s00204-008-0303-0 10.1186/1471-2199-7-33 10.1371/journal.pbio.1000412 10.1124/mol.54.1.86 10.1373/clinchem.2008.112797 10.1111/j.1600-0773.1993.tb01958.x 10.2144/00292rv02 10.1124/mol.107.037218 10.1038/sj.onc.1206238 10.1093/toxsci/kfm096 10.1016/j.ab.2012.06.010 10.1016/0378-4274(94)90139-2 10.1016/j.taap.2010.12.010 10.1016/j.cell.2012.09.019 10.1016/j.envint.2008.07.005 10.2478/10004-1254-61-2010-2024 10.1006/mcpr.2001.0376 10.1093/toxsci/kfl100 10.1158/0008-5472.CAN-04-0496 10.1126/science.1132939 10.1136/thorax.57.9.765 10.1093/bioinformatics/bts188 10.1186/gb-2002-3-7-research0034 10.1023/A:1016166127465 10.1128/MCB.00317-07 10.1016/0041-008X(84)90337-5 10.1080/15287399209531591 10.1186/1471-2164-9-419 10.1371/journal.pone.0018337 10.1016/j.taap.2012.02.001 10.1016/j.bbrc.2011.08.131 10.1016/0041-008X(85)90314-X 10.1016/j.taap.2009.01.005 10.1289/ehp.001081203 10.1101/gr.6.10.986 |
ContentType | Journal Article |
Copyright | Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved. |
Copyright_xml | – notice: Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved. |
DBID | FBQ CGR CUY CVF ECM EIF NPM AAYXX CITATION 7U7 8FD C1K FR3 P64 RC3 |
DOI | 10.1016/j.cbi.2013.06.008 |
DatabaseName | AGRIS Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed CrossRef Toxicology Abstracts Technology Research Database Environmental Sciences and Pollution Management Engineering Research Database Biotechnology and BioEngineering Abstracts Genetics Abstracts |
DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) CrossRef Genetics Abstracts Engineering Research Database Technology Research Database Toxicology Abstracts Biotechnology and BioEngineering Abstracts Environmental Sciences and Pollution Management |
DatabaseTitleList | Genetics Abstracts MEDLINE |
Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database – sequence: 3 dbid: FBQ name: AGRIS url: http://www.fao.org/agris/Centre.asp?Menu_1ID=DB&Menu_2ID=DB1&Language=EN&Content=http://www.fao.org/agris/search?Language=EN sourceTypes: Publisher |
DeliveryMethod | fulltext_linktorsrc |
Discipline | Anatomy & Physiology Chemistry Biology |
EISSN | 1872-7786 |
EndPage | 71 |
ExternalDocumentID | 10_1016_j_cbi_2013_06_008 23791969 US201500068738 |
Genre | Validation Studies Research Support, Non-U.S. Gov't Journal Article |
GrantInformation_xml | – fundername: Canadian Institutes of Health Research grantid: MOP-57903 |
GroupedDBID | --- --K --M -~X .GJ .~1 0R~ 1B1 1RT 1~. 1~5 29B 3O- 4.4 457 4G. 53G 5GY 5RE 5VS 6J9 7-5 71M 8P~ 9JM AACTN AAEDT AAEDW AAIAV AAIKJ AAKOC AALRI AAOAW AAQFI AAQXK AATCM AAXUO AAYJJ ABEFU ABFNM ABFRF ABFYP ABJNI ABLST ABMAC ABPIF ABPTK ABXDB ABYKQ ABZDS ACDAQ ACGFO ACGFS ACIUM ACRLP ADBBV ADEZE ADMUD AEBSH AEFWE AEKER AENEX AFFNX AFKWA AFTJW AFXIZ AGHFR AGUBO AGYEJ AHEUO AHHHB AI. AIEXJ AIKHN AITUG AJBFU AJOXV AKIFW ALCLG ALMA_UNASSIGNED_HOLDINGS AMFUW AMRAJ ASPBG AVWKF AXJTR AZFZN BKOJK BLECG BLXMC CS3 DU5 EBS EFJIC EJD EO8 EO9 EP2 EP3 F5P FBQ FDB FEDTE FGOYB FIRID FNPLU FYGXN G-2 G-Q GBLVA HMT HVGLF HZ~ H~9 IHE J1W KCYFY KOM M34 M41 MO0 N9A NCXOZ O-L O9- OAUVE OGGZJ OZT P-8 P-9 P2P PC. Q38 R2- RIG ROL RPZ SCC SDF SDG SDP SES SEW SPCBC SPT SSJ SSP SSZ T5K VH1 WH7 WUQ ZGI ZXP ~G- AAXKI AKRWK CGR CUY CVF ECM EIF NPM AAYXX ACRPL ADVLN AFJKZ CITATION 7U7 8FD C1K FR3 P64 RC3 |
ID | FETCH-LOGICAL-c401t-927aacc3b72c26cadec6d8a51b9b9d7bf2d6c98da9905c66ea00b142613939143 |
ISSN | 0009-2797 |
IngestDate | Sat Oct 05 04:29:35 EDT 2024 Fri Dec 06 06:04:55 EST 2024 Sat Sep 28 08:00:26 EDT 2024 Wed Dec 27 19:08:56 EST 2023 |
IsDoiOpenAccess | false |
IsOpenAccess | true |
IsPeerReviewed | true |
IsScholarly | true |
Issue | 1 |
Keywords | Quantitative real-time PCR C(q) Reference genes TCDD ARNT AHR 2,3,7,8-tetrachlorodibenzo-p-dioxin quantification cycle aryl hydrocarbon receptor normalized expression level aryl hydrocarbon receptor nuclear translocator NEL mRNA abundance Mouse model Normalization qPCR |
Language | English |
License | Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved. |
LinkModel | OpenURL |
MergedId | FETCHMERGED-LOGICAL-c401t-927aacc3b72c26cadec6d8a51b9b9d7bf2d6c98da9905c66ea00b142613939143 |
Notes | http://dx.doi.org/10.1016/j.cbi.2013.06.008 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
OpenAccessLink | https://doi.org/10.1016/j.cbi.2013.06.008 |
PMID | 23791969 |
PQID | 1512321654 |
PQPubID | 23462 |
PageCount | 9 |
ParticipantIDs | proquest_miscellaneous_1512321654 crossref_primary_10_1016_j_cbi_2013_06_008 pubmed_primary_23791969 fao_agris_US201500068738 |
PublicationCentury | 2000 |
PublicationDate | 2013-09-05 |
PublicationDateYYYYMMDD | 2013-09-05 |
PublicationDate_xml | – month: 09 year: 2013 text: 2013-09-05 day: 05 |
PublicationDecade | 2010 |
PublicationPlace | Ireland |
PublicationPlace_xml | – name: Ireland |
PublicationTitle | Chemico-biological interactions |
PublicationTitleAlternate | Chem Biol Interact |
PublicationYear | 2013 |
Publisher | Elsevier Ireland Ltd |
Publisher_xml | – name: Elsevier Ireland Ltd |
References | Kilkenny (10.1016/j.cbi.2013.06.008_b0080) 2010; 8 Boutros (10.1016/j.cbi.2013.06.008_b0035) 2011; 251 Linden (10.1016/j.cbi.2013.06.008_b0095) 2012; 428 Franc (10.1016/j.cbi.2013.06.008_b0065) 2008; 82 Lamb (10.1016/j.cbi.2013.06.008_b0085) 2006; 313 Silver (10.1016/j.cbi.2013.06.008_b0210) 2006; 7 Deindl (10.1016/j.cbi.2013.06.008_b0055) 2002; 236 Okey (10.1016/j.cbi.2013.06.008_b0135) 2007; 98 ATSDR (10.1016/j.cbi.2013.06.008_b0010) 1998 Schecter (10.1016/j.cbi.2013.06.008_b0185) 2006; 101 Pohjanvirta (10.1016/j.cbi.2013.06.008_b0145) 2009; 236 Poland (10.1016/j.cbi.2013.06.008_b0170) 1994; 46 Waggott (10.1016/j.cbi.2013.06.008_b0225) 2012; 28 Boverhof (10.1016/j.cbi.2013.06.008_b0040) 2006; 94 Longnecker (10.1016/j.cbi.2013.06.008_b0100) 2000; 11 Marinkovic (10.1016/j.cbi.2013.06.008_b0115) 2010; 61 Suzuki (10.1016/j.cbi.2013.06.008_b0215) 2000; 29 Heid (10.1016/j.cbi.2013.06.008_b0075) 1996; 6 Okey (10.1016/j.cbi.2013.06.008_b0140) 1994; 70 Yao (10.1016/j.cbi.2013.06.008_b0235) 2012; 260 Vandesompele (10.1016/j.cbi.2013.06.008_b0220) 2002; 3 Weisglas-Kuperus (10.1016/j.cbi.2013.06.008_b0230) 2000; 108 Michalek (10.1016/j.cbi.2013.06.008_b0125) 1992; 35 Falahatpisheh (10.1016/j.cbi.2013.06.008_b0060) 2003; 22 Pohjanvirta (10.1016/j.cbi.2013.06.008_b0165) 1998; 54 Yin (10.1016/j.cbi.2013.06.008_b0240) 2011; 413 Boutros (10.1016/j.cbi.2013.06.008_b0030) 2008; 9 Glare (10.1016/j.cbi.2013.06.008_b0070) 2002; 57 LifeTechnologies (10.1016/j.cbi.2013.06.008_b0090) 2012 Chapman (10.1016/j.cbi.2013.06.008_b0050) 1985; 78 Prokopec (10.1016/j.cbi.2013.06.008_b0175) 2013; 19 Andersen (10.1016/j.cbi.2013.06.008_b0005) 2004; 64 Seefeld (10.1016/j.cbi.2013.06.008_b0190) 1984; 73 Bertazzi (10.1016/j.cbi.2013.06.008_b0020) 1997; 8 Boutros (10.1016/j.cbi.2013.06.008_b0025) 2011; 6 Pohjanvirta (10.1016/j.cbi.2013.06.008_b0155) 2006; 160 Ren (10.1016/j.cbi.2013.06.008_b0180) 2010; 16 Bustin (10.1016/j.cbi.2013.06.008_b0045) 2009; 55 Pohjanvirta (10.1016/j.cbi.2013.06.008_b0160) 1993; 73 Selvey (10.1016/j.cbi.2013.06.008_b0195) 2001; 15 Mane (10.1016/j.cbi.2013.06.008_b0105) 2008; 19 McNulty (10.1016/j.cbi.2013.06.008_b0120) 1995; 212 Marguerat (10.1016/j.cbi.2013.06.008_b0110) 2012; 151 Moffat (10.1016/j.cbi.2013.06.008_b0130) 2007; 72 Shen (10.1016/j.cbi.2013.06.008_b0205) 2009; 35 Badghisi (10.1016/j.cbi.2013.06.008_b0015) 2002; 15 Pohjanvirta (10.1016/j.cbi.2013.06.008_b0150) 2012; 262 Shah (10.1016/j.cbi.2013.06.008_b0200) 2007; 27 |
References_xml | – volume: 11 start-page: 44 year: 2000 ident: 10.1016/j.cbi.2013.06.008_b0100 article-title: Serum dioxin level in relation to diabetes mellitus among Air Force veterans with background levels of exposure publication-title: Epidemiology doi: 10.1097/00001648-200001000-00010 contributor: fullname: Longnecker – volume: 262 start-page: 167 year: 2012 ident: 10.1016/j.cbi.2013.06.008_b0150 article-title: Unexpected gender difference in sensitivity to the acute toxicity of dioxin in mice publication-title: Toxicol. Appl. Pharmacol. doi: 10.1016/j.taap.2012.04.032 contributor: fullname: Pohjanvirta – volume: 19 start-page: 51 year: 2013 ident: 10.1016/j.cbi.2013.06.008_b0175 article-title: Systematic evaluation of medium-throughput mRNA abundance platforms publication-title: RNA doi: 10.1261/rna.034710.112 contributor: fullname: Prokopec – volume: 15 start-page: 799 year: 2002 ident: 10.1016/j.cbi.2013.06.008_b0015 article-title: Sequence mapping of epoxide adducts in human hemoglobin with LC–tandem MS and the SALSA algorithm publication-title: Chem. Res. Toxicol. doi: 10.1021/tx015589+ contributor: fullname: Badghisi – year: 1998 ident: 10.1016/j.cbi.2013.06.008_b0010 article-title: Toxicological profile for chlorinated dibenzo-p-dioxins contributor: fullname: ATSDR – volume: 101 start-page: 419 year: 2006 ident: 10.1016/j.cbi.2013.06.008_b0185 article-title: Dioxins: an overview publication-title: Environ. Res. doi: 10.1016/j.envres.2005.12.003 contributor: fullname: Schecter – volume: 19 start-page: 342 year: 2008 ident: 10.1016/j.cbi.2013.06.008_b0105 article-title: Systematic method for determining an ideal housekeeping gene for real-time PCR analysis publication-title: J. Biomol. Tech. contributor: fullname: Mane – volume: 212 start-page: 165 year: 1995 ident: 10.1016/j.cbi.2013.06.008_b0120 article-title: Transcriptional regulation of glyceraldehyde-3-phosphate dehydrogenase by 2,3,7,8-tetrachlorodibenzo-p-dioxin publication-title: Biochem. Biophys. Res. Commun. doi: 10.1006/bbrc.1995.1951 contributor: fullname: McNulty – volume: 160 start-page: 134 year: 2006 ident: 10.1016/j.cbi.2013.06.008_b0155 article-title: Evaluation of various housekeeping genes for their applicability for normalization of mRNA expression in dioxin-treated rats publication-title: Chem. Biol. Interact. doi: 10.1016/j.cbi.2006.01.001 contributor: fullname: Pohjanvirta – volume: 82 start-page: 809 year: 2008 ident: 10.1016/j.cbi.2013.06.008_b0065 article-title: Patterns of dioxin-altered mRNA expression in livers of dioxin-sensitive versus dioxin-resistant rats publication-title: Arch. Toxicol. doi: 10.1007/s00204-008-0303-0 contributor: fullname: Franc – year: 2012 ident: 10.1016/j.cbi.2013.06.008_b0090 contributor: fullname: LifeTechnologies – volume: 7 start-page: 33 year: 2006 ident: 10.1016/j.cbi.2013.06.008_b0210 article-title: Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR publication-title: BMC Mol. Biol. doi: 10.1186/1471-2199-7-33 contributor: fullname: Silver – volume: 8 start-page: e1000412 year: 2010 ident: 10.1016/j.cbi.2013.06.008_b0080 article-title: Improving bioscience research reporting: the ARRIVE guidelines for reporting animal research publication-title: PLoS Biol. doi: 10.1371/journal.pbio.1000412 contributor: fullname: Kilkenny – volume: 54 start-page: 86 year: 1998 ident: 10.1016/j.cbi.2013.06.008_b0165 article-title: Point mutation in intron sequence causes altered carboxyl-terminal structure in the aryl hydrocarbon receptor of the most 2,3,7,8-tetrachlorodibenzo-p-dioxin-resistant rat strain publication-title: Mol. Pharmacol. doi: 10.1124/mol.54.1.86 contributor: fullname: Pohjanvirta – volume: 55 start-page: 611 year: 2009 ident: 10.1016/j.cbi.2013.06.008_b0045 article-title: The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments publication-title: Clin. Chem. doi: 10.1373/clinchem.2008.112797 contributor: fullname: Bustin – volume: 73 start-page: 52 year: 1993 ident: 10.1016/j.cbi.2013.06.008_b0160 article-title: Comparative acute lethality of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), 1,2,3,7,8-pentachlorodibenzo-p-dioxin and 1,2,3,4,7,8-hexachlorodibenzo-p-dioxin in the most TCDD-susceptible and the most TCDD-resistant rat strain publication-title: Pharmacol. Toxicol. doi: 10.1111/j.1600-0773.1993.tb01958.x contributor: fullname: Pohjanvirta – volume: 29 start-page: 332 year: 2000 ident: 10.1016/j.cbi.2013.06.008_b0215 article-title: Control selection for RNA quantitation publication-title: Biotechniques doi: 10.2144/00292rv02 contributor: fullname: Suzuki – volume: 72 start-page: 956 year: 2007 ident: 10.1016/j.cbi.2013.06.008_b0130 article-title: Aryl hydrocarbon receptor splice variants in the dioxin-resistant rat: tissue expression and transactivational activity publication-title: Mol. Pharmacol. doi: 10.1124/mol.107.037218 contributor: fullname: Moffat – volume: 22 start-page: 2160 year: 2003 ident: 10.1016/j.cbi.2013.06.008_b0060 article-title: Ligand-activated Ahr signaling leads to disruption of nephrogenesis and altered Wilms’ tumor suppressor mRNA splicing publication-title: Oncogene doi: 10.1038/sj.onc.1206238 contributor: fullname: Falahatpisheh – volume: 98 start-page: 5 year: 2007 ident: 10.1016/j.cbi.2013.06.008_b0135 article-title: An aryl hydrocarbon receptor odyssey to the shores of toxicology: the Deichmann Lecture, International Congress of Toxicology-XI publication-title: Toxicol. Sci. doi: 10.1093/toxsci/kfm096 contributor: fullname: Okey – volume: 428 start-page: 81 year: 2012 ident: 10.1016/j.cbi.2013.06.008_b0095 article-title: Bayesian modeling of reproducibility and robustness of RNA reverse transcription and quantitative real-time polymerase chain reaction publication-title: Anal. Biochem. doi: 10.1016/j.ab.2012.06.010 contributor: fullname: Linden – volume: 70 start-page: 1 year: 1994 ident: 10.1016/j.cbi.2013.06.008_b0140 article-title: The Ah receptor: mediator of the toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds publication-title: Toxicol. Lett. doi: 10.1016/0378-4274(94)90139-2 contributor: fullname: Okey – volume: 251 start-page: 119 year: 2011 ident: 10.1016/j.cbi.2013.06.008_b0035 article-title: Hepatic transcriptomic responses to TCDD in dioxin-sensitive and dioxin-resistant rats during the onset of toxicity publication-title: Toxicol. Appl. Pharmacol. doi: 10.1016/j.taap.2010.12.010 contributor: fullname: Boutros – volume: 151 start-page: 671 year: 2012 ident: 10.1016/j.cbi.2013.06.008_b0110 article-title: Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells publication-title: Cell doi: 10.1016/j.cell.2012.09.019 contributor: fullname: Marguerat – volume: 35 start-page: 50 year: 2009 ident: 10.1016/j.cbi.2013.06.008_b0205 article-title: Dioxin-like compounds in agricultural soils near e-waste recycling sites from Taizhou area, China: chemical and bioanalytical characterization publication-title: Environ. Int. doi: 10.1016/j.envint.2008.07.005 contributor: fullname: Shen – volume: 61 start-page: 445 year: 2010 ident: 10.1016/j.cbi.2013.06.008_b0115 article-title: Dioxins and human toxicity publication-title: Arh. Hig. Rada Toksikol. doi: 10.2478/10004-1254-61-2010-2024 contributor: fullname: Marinkovic – volume: 15 start-page: 307 year: 2001 ident: 10.1016/j.cbi.2013.06.008_b0195 article-title: Beta-actin – an unsuitable internal control for RT-PCR publication-title: Mol. Cell. Probes doi: 10.1006/mcpr.2001.0376 contributor: fullname: Selvey – volume: 94 start-page: 398 year: 2006 ident: 10.1016/j.cbi.2013.06.008_b0040 article-title: Comparative toxicogenomic analysis of the hepatotoxic effects of TCDD in Sprague Dawley rats and C57BL/6 mice publication-title: Toxicol. Sci. doi: 10.1093/toxsci/kfl100 contributor: fullname: Boverhof – volume: 64 start-page: 5245 year: 2004 ident: 10.1016/j.cbi.2013.06.008_b0005 article-title: Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets publication-title: Cancer Res. doi: 10.1158/0008-5472.CAN-04-0496 contributor: fullname: Andersen – volume: 313 start-page: 1929 year: 2006 ident: 10.1016/j.cbi.2013.06.008_b0085 article-title: The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease publication-title: Science doi: 10.1126/science.1132939 contributor: fullname: Lamb – volume: 16 start-page: 1076 year: 2010 ident: 10.1016/j.cbi.2013.06.008_b0180 article-title: Selection of housekeeping genes for use in quantitative reverse transcription PCR assays on the murine cornea publication-title: Mol. Vis. contributor: fullname: Ren – volume: 8 start-page: 646 year: 1997 ident: 10.1016/j.cbi.2013.06.008_b0020 article-title: Dioxin exposure and cancer risk: a 15-year mortality study after the “Seveso accident” publication-title: Epidemiology contributor: fullname: Bertazzi – volume: 57 start-page: 765 year: 2002 ident: 10.1016/j.cbi.2013.06.008_b0070 article-title: Beta-actin and GAPDH housekeeping gene expression in asthmatic airways is variable and not suitable for normalising mRNA levels publication-title: Thorax doi: 10.1136/thorax.57.9.765 contributor: fullname: Glare – volume: 28 start-page: 1546 year: 2012 ident: 10.1016/j.cbi.2013.06.008_b0225 article-title: NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts188 contributor: fullname: Waggott – volume: 3 year: 2002 ident: 10.1016/j.cbi.2013.06.008_b0220 article-title: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes publication-title: Genome Biol. doi: 10.1186/gb-2002-3-7-research0034 contributor: fullname: Vandesompele – volume: 236 start-page: 139 year: 2002 ident: 10.1016/j.cbi.2013.06.008_b0055 article-title: Differential expression of GAPDH and beta3-actin in growing collateral arteries publication-title: Mol. Cell. Biochem. doi: 10.1023/A:1016166127465 contributor: fullname: Deindl – volume: 27 start-page: 4238 year: 2007 ident: 10.1016/j.cbi.2013.06.008_b0200 article-title: Peroxisome proliferator-activated receptor alpha regulates a microRNA-mediated signaling cascade responsible for hepatocellular proliferation publication-title: Mol. Cell. Biol. doi: 10.1128/MCB.00317-07 contributor: fullname: Shah – volume: 73 start-page: 311 year: 1984 ident: 10.1016/j.cbi.2013.06.008_b0190 article-title: Characterization of the wasting syndrome in rats treated with 2,3,7,8-tetrachlorodibenzo-p-dioxin publication-title: Toxicol. Appl. Pharmacol. doi: 10.1016/0041-008X(84)90337-5 contributor: fullname: Seefeld – volume: 35 start-page: 29 year: 1992 ident: 10.1016/j.cbi.2013.06.008_b0125 article-title: Investigation of TCDD half-life heterogeneity in veterans of Operation Ranch Hand publication-title: J. Toxicol. Environ. Health doi: 10.1080/15287399209531591 contributor: fullname: Michalek – volume: 9 start-page: 419 year: 2008 ident: 10.1016/j.cbi.2013.06.008_b0030 article-title: Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: comparison of rat and mouse publication-title: BMC Genomics doi: 10.1186/1471-2164-9-419 contributor: fullname: Boutros – volume: 6 start-page: e18337 year: 2011 ident: 10.1016/j.cbi.2013.06.008_b0025 article-title: MRNA levels in control rat liver display strain-specific, hereditary, and AHR-dependent components publication-title: PLoS ONE doi: 10.1371/journal.pone.0018337 contributor: fullname: Boutros – volume: 260 start-page: 135 year: 2012 ident: 10.1016/j.cbi.2013.06.008_b0235 article-title: Inter-strain heterogeneity in rat hepatic transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin publication-title: Toxicol. Appl. Pharmacol. doi: 10.1016/j.taap.2012.02.001 contributor: fullname: Yao – volume: 413 start-page: 537 year: 2011 ident: 10.1016/j.cbi.2013.06.008_b0240 article-title: Systematic selection of housekeeping genes for gene expression normalization in chicken embryo fibroblasts infected with Newcastle disease virus publication-title: Biochem. Biophys. Res. Commun. doi: 10.1016/j.bbrc.2011.08.131 contributor: fullname: Yin – volume: 78 start-page: 147 year: 1985 ident: 10.1016/j.cbi.2013.06.008_b0050 article-title: Dose-related effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in C57BL/6J and DBA/2J mice publication-title: Toxicol. Appl. Pharmacol. doi: 10.1016/0041-008X(85)90314-X contributor: fullname: Chapman – volume: 236 start-page: 166 year: 2009 ident: 10.1016/j.cbi.2013.06.008_b0145 article-title: Transgenic mouse lines expressing rat AH receptor variants–a new animal model for research on AH receptor function and dioxin toxicity mechanisms publication-title: Toxicol. Appl. Pharmacol. doi: 10.1016/j.taap.2009.01.005 contributor: fullname: Pohjanvirta – volume: 108 start-page: 1203 year: 2000 ident: 10.1016/j.cbi.2013.06.008_b0230 article-title: Immunologic effects of background exposure to polychlorinated biphenyls and dioxins in Dutch preschool children publication-title: Environ. Health Perspect. doi: 10.1289/ehp.001081203 contributor: fullname: Weisglas-Kuperus – volume: 46 start-page: 915 year: 1994 ident: 10.1016/j.cbi.2013.06.008_b0170 article-title: Analysis of the four alleles of the murine aryl hydrocarbon receptor publication-title: Mol. Pharmacol. contributor: fullname: Poland – volume: 6 start-page: 986 year: 1996 ident: 10.1016/j.cbi.2013.06.008_b0075 article-title: Real time quantitative PCR publication-title: Genome Res. doi: 10.1101/gr.6.10.986 contributor: fullname: Heid |
SSID | ssj0000240 |
Score | 2.143798 |
Snippet | BACKGROUND: Quantitative real-time PCR (qPCR) is the “gold-standard” technique for measuring mRNA abundances. To correctly compare samples and generate... Quantitative real-time PCR (qPCR) is the "gold-standard" technique for measuring mRNA abundances. To correctly compare samples and generate biologically valid... Background: Quantitative real-time PCR (qPCR) is the agold-standarda technique for measuring mRNA abundances. To correctly compare samples and generate... |
SourceID | proquest crossref pubmed fao |
SourceType | Aggregation Database Index Database Publisher |
StartPage | 63 |
SubjectTerms | Algorithms animal models Animals data collection essential genes Female Gene Expression - drug effects Genes, Essential - drug effects genotype Hypoxanthine Phosphoribosyltransferase - genetics Male messenger RNA Mice Mice, Inbred C57BL Mice, Inbred DBA Mice, Transgenic Multivariate Analysis Peptide Elongation Factor 1 - genetics Polychlorinated Dibenzodioxins - toxicity quantitative polymerase chain reaction Real-Time Polymerase Chain Reaction RNA, Messenger - genetics RNA, Messenger - metabolism tetrachlorodibenzo-p-dioxin toxicity toxins variance |
Title | Validating reference genes within a mouse model system of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity |
URI | https://www.ncbi.nlm.nih.gov/pubmed/23791969 https://search.proquest.com/docview/1512321654 |
Volume | 205 |
hasFullText | 1 |
inHoldings | 1 |
isFullTextHit | |
isPrint | |
link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3db9MwELe6IQQvCDbYypeMhBCwusqcNo4ftw408TAh0aK9RbbjbBlqUpVUgj3wT_APc2fnowOGgIdEkd0mku-n89357neEPDfCWvAbODNaBWwkR5rFsO2wFFttjzKLRjlmW5xEx7PRu9Pxaa_3fS1raVXpobn8bV3J_0gVxkCuWCX7D5JtXwoD8AzyhTtIGO5_JeOPYERjeQK2C2oJY89Qe7n4al7sqT107a1veFPTNqN9yGFpQ7gEXDGrbLVU5hxc9zLNtS0uS7ZgaV5-yREa8XRydITRgwoGTF5dOQj2hAMl82ROTuLIQLH09RKtwf5-WX4qF9asJZbltss2PlyZpvIGoInu9ueuHXS9QZ5goAn-1Fqvk_M6nRhru21Rx3vrCAZ2k5As8EfZ1mvdWKCZX3Ni12qZ1z9Zx59Xsl4j_qL7fRjiYmh0jil7oeNldaQR1RoWFnMHBh4KicxA3TbYJic2UxvkBrIrYkOG4bcubwhJ4ZrjcZco-NP3kF66fsMVW2cjU-X1bowzZ6Z3yZ3aD6EHHlT3SM8WW2T7oFBVOf9KX1CXGeyOXLbIzcPm6dak6Q-4TeYd-miLPurQRz36qKIOfdShj3r00TKjfBAOxOCPuKMvEXWvaIO5-2T29s10cszq5h3MgMteMcmFUsaEWnDDI6z1MFEaq_G-llqmQmc8jYyMUwXm0NhEkVVBgAFJMC9lKEFTPCCbRVnYXUKVUDzgmQpibUZZGsvxOBQZnuBLzWW23yevm2VOFp6jJWmSFy8SEE-C4klcAmfcJ7sgiESdwR6azD5wjPhhnZQIYepZI50E1hJPzlRhYZ0SNItDjoV_fbLjxdZ-qRH2w2tnHpHbHewfk81qubJPwJSt9FMHrR8ANpoz |
link.rule.ids | 314,780,784,27924,27925 |
linkProvider | Elsevier |
openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Validating+reference+genes+within+a+mouse+model+system+of+2%2C3%2C7%2C8-tetrachlorodibenzo-p-dioxin+%28TCDD%29+toxicity&rft.jtitle=Chemico-biological+interactions&rft.au=Prokopec%2C+Stephenie+D&rft.au=Buchner%2C+Nicholas+B&rft.au=Fox%2C+Natalie+S&rft.au=Chong%2C+Lauren+C&rft.date=2013-09-05&rft.eissn=1872-7786&rft.volume=205&rft.issue=1&rft.spage=63&rft_id=info:doi/10.1016%2Fj.cbi.2013.06.008&rft_id=info%3Apmid%2F23791969&rft.externalDocID=23791969 |
thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0009-2797&client=summon |
thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0009-2797&client=summon |
thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0009-2797&client=summon |