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Tables Available through DRG (listed alphabetically by author):

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1

Albertson DN, Pruetz B, Schmidt CJ, Kuhn DM, Kapatos G, Bannon MJ. (2004) Gene expression profile of the nucleus accumbens of human cocaine abusers: evidence for dysregulation of myelin.   J Neurochem. 2004 Mar;88(5):1211-9. http://www.ncbi.nlm.nih.gov/pubmed/15009677 

Table 2 Transcripts differentially expressed in the majority of cocaine users

 

Yes

2

Albertson DN, Schmidt CJ, Kapatos G, Bannon MJ. (2006) Distinctive profiles of gene expression in the human nucleus accumbens associated with cocaine and heroin abuse.   Neuropsychopharmacology. 2006 Oct;31(10):2304-12. Epub 2006 May 3. http://www.ncbi.nlm.nih.gov/pubmed/16710320 

Table 2 Genes Significantly Altered in Both the Heroin and Cocaine Abusers

 

Yes

 

 

Supplementary Table 1 (xls 118K)All transcripts significantly different in abundance between the majority of heroin subjects and their matched controls

 

Yes

3

Ammon S, Mayer P, Riechert U, Tischmeyer H, Höllt V. (2003) Microarray analysis of genes expressed in the frontal cortex of rats chronically treated with morphine and after naloxone precipitated withdrawal. Brain Res Mol Brain Res. 2003 Apr 10;112(1-2):113-25. http://www.ncbi.nlm.nih.gov/pubmed/12670709 

Table 2. Results DNA microarrays: chronic morphine treatment vs. saline treatment (control)

 

Yes

 

 

Table 3. Results DNA-microarrays: naloxone precipitated morphine withdrawal vs. saline treatment (control)

 

Yes

4

Anghel A, Jamieson CA, Ren X, Young J, Porche R, Ozigbo E, Ghods DE, Lee ML, Liu Y, Lutfy K, Friedman TC. (2010) Gene expression profiling following short-term and long-term morphine exposure in mice uncovers genes involved in food intake. Neuroscience. 2010 May 5;167(2):554-66. Epub 2010 Feb 6. http://www.ncbi.nlm.nih.gov/pubmed/20144693

Table 2. Hypothalamic genes with highest fold regulation by morphine  

 

Yes

 

 

Table 3. Pituitary genes with highest fold regulation by morphine

 

Yes

 

 

Table 4. Genes involved in the food intake pathway as elucidated by microarray analysis

 

Yes

 

 

Table 5. Real-time RT-PCR results compared with microarray data (expressed as percent of control)

 

Yes

5

Befort K, Filliol D, Darcq E, Ghate A, Matifas A, Lardenois A, Muller J, Thibault C, Dembele D, Poch O, Kieffer BL. (2008) Gene expression is altered in the lateral hypothalamus upon activation of the mu opioid receptor. Ann N Y Acad Sci. 2008;1129:175-84. http://www.ncbi.nlm.nih.gov/pubmed/18591478

TABLE 2. Mu opioid receptor-dependent genes regulated by chronic morphine in the lateral hypothalamus (LH)

Yes

 

 

TABLE 3. qPCR analysis of chronic morphine treatments for selected LH genes

 

Yes

6

Caster JM, Kuhn CM. (2009) Maturation of coordinated immediate early gene expression by cocaine during adolescence. Neuroscience. 2009 Apr 21;160(1):13-31. Epub 2009 Jan 7. http://www.ncbi.nlm.nih.gov/sites/pubmed/19245875

Table 1. Mean density values for striatal c-fos and zif268 mRNA levels http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668738/table/T1/

 

Yes

 

 

Table 2. Mean density values for cortical c-fos and zif268 mRNA levels http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668738/table/T2/

 

Yes

 

 

Table 3. Effect of saline injection in a novel environment on basal zif268 expression http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668738/table/T3/

 

Yes

7

Chen X, Che Y, Zhang L, Putman AH, Damaj I, Martin BR, Kendler KS, Miles MF. (2007) RhoA, encoding a Rho GTPase, is associated with smoking initiation.  Genes Brain Behav. 2007 Nov;6(8):689-97. Epub 2006 Dec 20. http://www.ncbi.nlm.nih.gov/pubmed/17284169 

Table S1.  Genes with significant alterations in expression following acute nicotine treatment in VTA. http://www3.interscience.wiley.com/journal/118529476/suppinfo
sm003.doc (65k) (Microsoft Word)

 

Yes

8

Couceyro P, Douglass J. (1995) Precipitated Morphine Withdrawal Stimulates Multiple Activator Protein-1 Signaling Pathways in Rat Brain Mol Pharmacol. 1995 Jan;47(1):29-39.  http://www.ncbi.nlm.nih.gov/pubmed/7838131 

TABLE 1  - Relative lntensity of c-fos mRNA signals in rat brain 1 hr after naloxone-precipitated morphine withdrawal http://molpharm.aspetjournals.org/content/47/1/29.long 

 

Yes

9

Edenberg HJ, Strother WN, McClintick JN, Tian H, Stephens M, Jerome RE, Lumeng L, Li TK, McBride WJ. (2005) Gene expression in the hippocampus of inbred alcohol-preferring and -nonpreferring rats. Genes Brain Behav. 2005 Feb;4(1):20-30. http://www.ncbi.nlm.nih.gov/pubmed/15660665

Table 3: Genes expressed at significantly (P < /= 0.01) higher levels in hippocampus of iP than iNP rats

 

Yes

 

 

Table 4: Genes expressed at significantly (P < /= 0.01) lower levels in the hippocampus of iP than iNP rats

 

Yes

 

 

Table S1. Genes that significantly differ (p < / = 0.05) between iP and iNP rat hippocampi http://onlinelibrary.wiley.com/doi/10.1111/j.1601-183X.2004.00091.x/suppinfo

 

Yes

10

Flatscher-Bader T, van der Brug M, Hwang JW, Gochee PA, Matsumoto I, Niwa S, Wilce PA. (2005) Alcohol-responsive genes in the frontal cortex and nucleus accumbens of human alcoholics.  J Neurochem. 2005 Apr;93(2):359-70. http://www.ncbi.nlm.nih.gov/pubmed/15816859 

Table 3 Differentially expressed genes common to both the NA and PFC.

 

Yes

 

 

Table 4 Comparison of gene expression of selected genes using microarray and RT-PCR.

 

Yes

 

 

Table 5 Differentially expressed genes in the PFC in major functional groups.

 

Yes

 

 

Table 6 Genes differentially expressed in the alcoholic NA in major functional groups.

 

Yes

11

Frohmader KS, Wiskerke J, Wise RA, Lehman MN, Coolen LM. (2010) Methamphetamine acts on subpopulations of neurons regulating sexual behavior in male rats. Neuroscience. 2010 Mar 31;166(3):771-84. Epub 2010 Jan 4. http://www.ncbi.nlm.nih.gov/pubmed/20045448 

Table 2. Overview of mating-induced Fos and Meth-induced pERK expression in brain areas where sex and activate non-overlapping neural populations

 

Yes

 

 

Table 3. Overview of mating-induced Fos and Meth-induced pERK expression in brain areas where neural activation was induced only by mating

 

Yes

 

 

Fig. 2. Sex-induced Fos and Meth-induced pERK expression in NAc, BLA, and ACA neurons 10 min following administration of 4 mg/kg Meth.

 

Yes

 

 

Fig. 4. Sex-induced Fos and Meth-induced pERK expression in NAc, BLA, and ACA neurons 15 min following administration of 4 mg/kg Meth.

 

Yes

12

Gass JT, Olive MF. (2008) Transcriptional profiling of the rat frontal cortex following administration of the mGlu5 receptor antagonists MPEP and MTEP. Eur J Pharmacol. 2008 Apr 28;584(2-3):253-62. Epub 2008 Feb 20. http://www.ncbi.nlm.nih.gov/pubmed/18346726

Table 1 List of genes changed by MPEP and MTEP

 

Yes

 

 

Table 3 Results of qPCR analysis of 9 selected genes from microarray findings.

 

Yes

13

Grice DE, Reenilä I, Männistö PT, Brooks AI, Smith GG, Golden GT, Buxbaum JD, Berrettini WH. (2007) Transcriptional profiling of C57 and DBA strains of mice in the absence and presence of morphine BMC Genomics. 2007 Mar 16;8:76. http://www.ncbi.nlm.nih.gov/pubmed/17367521

Additional file 1. STable1. The data provided represent genes showing differential expression. A. Genes showing differential expression between vehicle-treated C57 and DBA strains. B. Genes showing differential expression between morphine-treated C57 and DBA strains. C. Genes showing differential expression between vehicle and morphine-treated DBA. http://www.biomedcentral.com/1471-2164/8/76/suppl/S1

 

Yes

14

Jayanthi S, McCoy MT, Beauvais G, Ladenheim B, Gilmore K, Wood W 3rd, Becker K, Cadet JL. (2009) Methamphetamine Induces Dopamine D1 Receptor-Dependent Endoplasmic Reticulum Stress-Related Molecular Events in the Rat Striatum PLoS One. 2009 Jun 30;4(6):e6092. http://www.ncbi.nlm.nih.gov/pubmed/19564919 

Table S3. List of 173 SCH23390-sensitive METH-responsive genes in the rat striatum.
(0.07 MB XLS)

 

Yes

 

 

Table S4. List of 372 SCH23390-resistant METH-responsive genes in the rat striatum. (0.12 MB XLS)

 

Yes

 

 

Table 1 METH administration causes changes in ER stress-related genes.

 

Yes

15

Kily LJ, Cowe YC, Hussain O, Patel S, McElwaine S, Cotter FE, Brennan CH. (2008) Gene expression changes in a zebrafish model of drug dependency suggest conservation of neuro-adaptation pathways.
J Exp Biol. 2008 May;211(Pt 10):1623-34. http://www.ncbi.nlm.nih.gov/pubmed/18456890

Table 3.  Shared genes showing significant changes in expression between control and drug treated fish http://jeb.biologists.org/cgi/content-nw/full/211/10/1623/TBL3 

 

Yes

 

 

Table S1.  Genes showing significant 1.5-fold or greater changes in expression in both ethanol-treated and nicotine-treated animals compared with control animals http://jeb.biologists.org/cgi/data/211/10/1623/DC1/1 

 

Yes

 

 

Table S2.  Genes showing twofold changes in expression in both ethanol-treated and nicotine-treated animals compared with control animals grouped according to biological process http://jeb.biologists.org/cgi/data/211/10/1623/DC1/1 

 

Yes

16

Korostynski M, Kaminska-Chowaniec D, Piechota M, Przewlocki R. (2006) Gene expression profiling in the striatum of inbred mouse strains with distinct opioid-related phenotypes.  BMC Genomics. 2006 Jun 13;7:146. http://www.ncbi.nlm.nih.gov/pubmed/16772024 

Additional File 2 Click here for file

 

Yes

 

 

Additional File 3 Click here for file(80K, xls)

 

Yes

 

 

Table 3 Gene expression results obtained by microarrays and qPCR.

 

Yes

17

Korostynski M, Piechota M, Kaminska D, Solecki W, Przewlocki R. (2007) Morphine effects on striatal transcriptome in mice. Genome Biol. 2007;8(6):R128. http://www.ncbi.nlm.nih.gov/pubmed/17598886

Additional data file 1Click here for file(465K, xls)

 

Yes

 

 

Additional data file 2Click here for file(223K, xls)

 

Yes

 

 

Additional data file 3Click here for file(107K, xls)

 

Yes

 

 

Additional data file 4Click here for file(32K, xls)

 

Yes

 

 

Additional data file 5Click here for file(367K, xls)

 

Yes

18

Krasnova IN, Li SM, Wood WH, McCoy MT, Prabhu VV, Becker KG, Katz JL, Cadet JL. (2008) Transcriptional responses to reinforcing effects of cocaine in the rat hippocampus and cortex.   Genes Brain Behav. 2008 Mar;7(2):193-202. Epub 2007 Jul 19. http://www.ncbi.nlm.nih.gov/pubmed/17640290 

Table 1: Genes significantly changed after cocaine CPP treatment in the hippocampus

 

Yes

 

 

Table 2 : Reverse transcriptase--polymerase chain reaction confirmation for selected genes changed after cocaine CPP treatment in the hippocampus and cortex

 

Yes

 

 

Table S1: Hippocampus 17 K microarray data .
sm001.xls (7444k) (Microsoft Excel)


Yes

 

 

Table S2: Hippocampus MGC microarray data .
sm002.xls (4314k) (Microsoft Excel)

\\

Yes

 

 

Table S3: Cortex 17 K microarray data.
sm003.xls (8573k) (Microsoft Excel)

\\

Yes

 

 

Table S4: Cortex MGC microarray data.
sm004.xls (4697k) (Microsoft Excel)


Yes

 

 

Table S5: Genes significantly changed after cocaine-CPP treatment in the frontal cortex.
sm005.doc (27k) (Microsoft Word)


Yes

19

Lehrmann E, Colantuoni C, Deep-Soboslay A, Becker KG, Lowe R, Huestis MA, Hyde TM, Kleinman JE, Freed WJ. (2006) Transcriptional changes common to human cocaine, cannabis and phencyclidine abuse.   PLoS One. 2006 Dec 27;1:e114. http://www.ncbi.nlm.nih.gov/pubmed/17205118 

TableS2  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1762434/?tool=pubmed#s5
Full list of significantly regulated transcripts in postmortem aPFC from cocaine, phencyclidine and/or cannabis abusers. One-hundred and thirty-nine transcripts were significantly regulated by group average p-value (GAP) criteria. Overweight/obese controls with cardiovascular disease (CVDC) compared to normal/overweight controls (Table S1) illustrated that drug-induced cellular stress was not an underlying cause in the common transcriptional patterns in the drug abuse cases. Gene symbols were annotated using GenBank Accession numbers and EntrezGene.
(0.06 MB DOC) Click here for additional data file.(63K, doc) 

 

Yes

20

Lehrmann E, Oyler J, Vawter MP, Hyde TM, Kolachana B, Kleinman JE, Huestis MA, Becker KG, Freed WJ. (2003) Transcriptional profiling in the human prefrontal cortex: evidence for two activational states associated with cocaine abuse. Pharmacogenomics J. 2003;3(1):27-40. http://www.ncbi.nlm.nih.gov/pubmed/12629581

Table 2 Mean p-value and z-ratio scores for 65 selected transcripts

 

Yes

21

Lewohl JM, Wang L, Miles MF, Zhang L, Dodd PR, Harris RA. (2000) Gene expression in human alcoholism: microarray analysis of frontal cortex.  Alcohol Clin Exp Res. 2000 Dec;24(12):1873-82.  http://www.ncbi.nlm.nih.gov/pubmed/11141048 

Table 2.  Myelin-Related Expression Data http://www3.interscience.wiley.com/cgi-bin/fulltext/119040167/PDFSTART 

 

Yes

 

 

Table 3.  Genes That Meet the Criteria for Differential Expression on the cDNA (GS-1, GS-2) Array http://www3.interscience.wiley.com/cgi-bin/fulltext/119040167/PDFSTART

 

Yes

 

 

Table 4.  Genes That Meet the Criteria for Differential Expression on the Oligonucleotide (A-1, A-2) Arrays http://www3.interscience.wiley.com/cgi-bin/fulltext/119040167/PDFSTART 

 

Yes

22

Liu J, Lewohl JM, Harris RA, Iyer VR, Dodd PR, Randall PK, Mayfield RD. (2006) Patterns of gene expression in the frontal cortex discriminate alcoholic from nonalcoholic individuals. Neuropsychopharmacology. 2006 Jul;31(7):1574-82. Epub 2005 Nov 2. http://www.ncbi.nlm.nih.gov/sites/entrez/16292326

Supplemental Table 6 (xls 66K)
Table 6. Full list of identified genes (531 genes). Green indicates down-regulation and red for up-regulation in alcoholic group.

 

Yes

 

 

Supplemental Table 7 (xls 46K)
Table 7. List of genes in each functional group.

 

Yes

23

Loguinov AV, Anderson LM, Crosby GJ, Yukhananov RY. (2001) Gene expression following acute morphine administration Physiol Genomics. 2001 Aug 28;6(3):169-81. http://www.ncbi.nlm.nih.gov/pubmed/11526201 

Fig. 4. Table of the genes selected using regression clustering. Data from Table 1.  Up- and downregulated genes http://physiolgenomics.physiology.org/cgi/content-nw/full/6/3/169/T1  included.

 

Yes

24

Luo Y, Sarabi SA, Backman C, Shan L, Hoffer B, Federoff H. (2009) Brain Res. 2009 Dec 11;1302:42-53. Epub 2009 Sep 16. Expression pattern of NuIP gene in adult mouse brain.  http://www.ncbi.nlm.nih.gov/pubmed/19765553 

Table 1. Summary of brain areas expressing NuIP protein and Nurr1.

 

Yes

25

Lynch WJ, Girgenti MJ, Breslin FJ, Newton SS, Taylor JR. (2008) Gene profiling the response to repeated cocaine self-administration in dorsal striatum: a focus on circadian genes.  Brain Res. 2008 Jun 5;1213:166-77. Epub 2008 Mar 15. http://www.ncbi.nlm.nih.gov/pubmed/18452895 

Table 1. Genes that were identified as being differentially regulated in the rat striatum following cocaine self-administration. (A) Genes identified as upregulated in the striatum following cocaine self-administration using microarray. (B) Genes identified as(more ...)

 

Yes

 

 

Table 2. Circadian genes and genes regulated by/associated with the circadian system that were identified as being differentially regulated in the rat striatum following cocaine self-administration. (A) Genes identified as upregulated in the striatum following(more ...)

 

Yes

 

 

Supplementary Material Click here to view .(1.8M, xls) 

 

Yes

26

Mann A, Miksys S, Lee A, Mash DC, Tyndale RF. (2008) Induction of the drug metabolizing enzyme CYP2D in monkey brain by chronic nicotine treatment.  Neuropharmacology. 55(7):1147-55. Epub 2008 Jul 19.  http://www.ncbi.nlm.nih.gov/pubmed/18687346 

Table 2. Brain CYP2D protein immunocytochemical staining in saline- and chronic nicotine-treated monkeys

 

Yes

27

Marie-Claire C, Courtin C, Robert A, Gidrol X, Roques BP, Noble F. (2007) Sensitization to the conditioned rewarding effects of morphine modulates gene expression in rat hippocampus.  Neuropharmacology. 2007 Feb;52(2):430-5. Epub 2006 Oct 2. http://www.ncbi.nlm.nih.gov/pubmed/17014870 

Table 1 Genes that are regulated by chronic morphine in rat hippocampus based on microarray analysis. Data are the mean of 6 hybridizations.

 

Yes

28

Mayfield RD, Lewohl JM, Dodd PR, Herlihy A, Liu J, Harris RA. (2002) Patterns of gene expression are altered in the frontal and motor cortices of human alcoholics.  J Neurochem. 2002 May;81(4):802-13. http://www.ncbi.nlm.nih.gov/pubmed/12065639  

http://onlinelibrary.wiley.com/doi/10.1046/j.1471-4159.2002.00860.x/full#ss8http://onlinelibrary.wiley.com/doi/10.1046/j.1471-4159.2002.00860.x/full#t4Table 4 Differential expression values for genes involved in global processes http://www3.interscience.wiley.com/cgi-bin/fulltext/118943183/PDFSTART

 

Yes

 

 

http://onlinelibrary.wiley.com/doi/10.1046/j.1471-4159.2002.00860.x/full#ss8http://onlinelibrary.wiley.com/doi/10.1046/j.1471-4159.2002.00860.x/full#t5Table 5 Differential expression values for genes involved in specific signaling processes http://www3.interscience.wiley.com/cgi-bin/fulltext/118943183/PDFSTART

 

Yes

29

Maze I, Covington HE 3rd, Dietz DM, LaPlant Q, Renthal W, Russo SJ, Mechanic M, Mouzon E, Neve RL, Haggarty SJ, Ren Y, Sampath SC, Hurd YL, Greengard P, Tarakhovsky A, Schaefer A, Nestler EJ. (2010) Essential role of the histone methyltransferase G9a in cocaine-induced plasticity. Science. 2010 Jan 8;327(5962):213-6. http://www.ncbi.nlm.nih.gov/pubmed/20056891

Table S1. Gene List: Acute (94 Genes) http://www.sciencemag.org/cgi/content/full/327/5962/213/DC1

 

Yes

 

 

Table S2. Gene List: Repeated + Acute (277 Genes) http://www.sciencemag.org/cgi/content/full/327/5962/213/DC1

 

Yes

 

 

Table S3. Gene List: Repeated WD + Acute (217 Genes) http://www.sciencemag.org/cgi/content/full/327/5962/213/DC1

 

Yes

 

 

Table S4. Effect of G9a overexpression on genes that display increased mRNA induction in NAc following repeated cocaine. http://www.sciencemag.org/cgi/content/full/327/5962/213/DC1

 

Yes

30

McClung CA, Nestler EJ, Zachariou V. (2005) Regulation of gene expression by chronic morphine and morphine withdrawal in the locus ceruleus and ventral tegmental area.  J Neurosci. 25(25):6005-15. http://www.ncbi.nlm.nih.gov/pubmed/15976090 

supplemental material Tables S1-S5 (Two S4’s)

 

Yes

31

McClung CA, Nestler EJ. (2003) Regulation of gene expression and cocaine reward by CREB and DeltaFosB. Nat Neurosci. 6(11):1208-15. Epub 2003 Oct 19. http://www.ncbi.nlm.nih.gov/pubmed/14566342

Supplementary Table 1(pdf 22K)

Supplementary Tables

Yes

 

 

Supplementary Table 2(pdf 20K)

Supplementary Tables

Yes

 

 

Supplementary Table 3(pdf 23K)

Supplementary Tables

Yes

 

 

Supplementary Table 4(pdf 18K)

Supplementary Tables

Yes

 

 

Supplementary Table 5(pdf 21K)

Supplementary Tables

Yes

 

 

Supplementary Table 6(pdf 21K)

Supplementary Tables

Yes

 

 

Supplementary Table 7(pdf 20K)

Supplementary Tables

Yes

 

 

Supplementary Table 8(pdf 20K)

Supplementary Tables

Yes

 

 

Supplementary Table 9(pdf 24K)

Supplementary Tables

Yes

 

 

Supplementary Table 10(pdf 21K)

Supplementary Tables

Yes

 

 

Supplementary Table 11(pdf 64K)

Supplementary Tables

Yes

 

 

Supplementary Table 12(pdf 65K)

Supplementary Tables

Yes

 

 

Table 2. Functional clusters of genes upregulated by CREB and FosB


Yes

*32

Renthal W, Kumar A, Xiao G, Wilkinson M, Covington HE 3rd, Maze I, Sikder D, Robison AJ, LaPlant Q, Dietz DM, Russo SJ, Vialou V, Chakravarty S, Kodadek TJ, Stack A, Kabbaj M, Nestler EJ.(2009) Genome-wide Analysis of Chromatin Regulation by Cocaine Reveals a Role for Sirtuins  Neuron. 2009 May 14;62(3):335-48..http://www.ncbi.nlm.nih.gov/pubmed/19447090

Table S1. Cocaine Regulation of H3 Acetylation.

Out of order

Yes

 

 

Table S2. Cocaine Regulation of H4 Acetylation.

 

Yes

 

 

Table S3. Cocaine Regulation of Both H3 and H4 Acetylation.

 

Yes

 

 

Table S4. Cocaine Regulation of Dimethyl-K9/K27 H3.

 

Yes

 

 

Table S5. Cocaine Regulation of Histone Acetylation and Methylation.

 

Yes

 

 

Table S6. DeltaFosB Target Genes in Chronic Cocaine-Treated Mice.

 

Yes

 

 

Table S7. DeltaFosB Target Genes in Chronic Saline-Treated Mice.

 

Yes

 

 

Table S8. Cocaine Regulation of Histone Modifications at DeltaFosB Target Genes.

 

Yes

33

McClung CA, Sidiropoulou K, Vitaterna M, Takahashi JS, White FJ, Cooper DC, Nestler EJ. (2005) Regulation of dopaminergic transmission and cocaine reward by the Clock gene. Proc Natl Acad Sci U S A. 102(26):9377-81. Epub 2005 Jun 20. http://www.ncbi.nlm.nih.gov/pubmed/15967985

Table 1. Genes that are regulated in the VTA of Clock mutant mice vs. wild-type littermate controls that may directly affect dopaminergic transmission or are known to be involved in circadian rhythms

 

Yes

 

 

Supporting Table 2 Genes regulated in the VTA of Clock mutant mice

 

Yes

34

Mexal S, Frank M, Berger R, Adams CE, Ross RG, Freedman R, Leonard S. (2005) Differential modulation of gene expression in the NMDA postsynaptic density of schizophrenic and control smokers.  Brain Res Mol Brain Res. 2005 Oct 3;139(2):317-32. http://www.ncbi.nlm.nih.gov/pubmed/16122832

Table 4. Genes groups differentially expressed between smokers and nonsmokers (P < 0.05)

 

Yes

 

 

Table 6. QRT-PCR confirmation of microarray gene expression changes

 

Yes

 

 

Supplemental Table 2. Probe sets on the Affymetrix U95Av2 chips for genes expressed in the NMDA postsynaptic density
Download this File (88 K) 

 

Yes

 

 

Supplementary Table 3. All genes differentially expressed between smokers and nonsmokers (P < 0.05)
Download this File (405 K) 

 

Yes

 

 

Supplementary Table 4. All genes differentially expressed by the interaction of schizophrenia × smoking
Download this File (102 K) 

 

Yes

35

Mitchell ES, Snyder-Keller A. (2003) c-fos and cleaved caspase-3 expression after perinatal exposure to ethanol, cocaine, or the combination of both drugs. Brain Res Dev Brain Res. 2003 Dec 30;147(1-2):107-17. http://www.ncbi.nlm.nih.gov/pubmed/14741756

Fig. 3. Striatal c-fos induction in E22 fetuses: prenatal ethanol and cocaine treatments.

 

Yes

 

 

Table 1. Fos expression in neonatal rats at 0, 3, and 24 h after C-section

 

Yes

 

 

Table 2. Caspase-3 expression in neonatal rats at 0, 3, and 24 h after C-section

 

Yes

 

 

Fig. 6. Striatal caspase-3 induction in E22 fetuses: prenatal ethanol and cocaine treatments.

 

Yes

36

Mitrano DA, Arnold C, Smith Y. (2008) Subcellular and subsynaptic localization of group I metabotropic glutamate receptors in the nucleus accumbens of cocaine-treated rats. Neuroscience. 2008 Jun 23;154(2):653-66. Epub 2008 Mar 29. http://www.ncbi.nlm.nih.gov/sites/pubmed/18479833

Table 1. Subsynaptic group I mGluRs labeling after cocaine treatment in the accumbens core. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2517176/table/T1/ 

 

Yes

 

 

Table 2. Subsynaptic group I mGluRs labeling after cocaine treatment in the accumbens shell. http://physiolgenomics.physiology.org/cgi/content-nw/full/23/1/89/T2 

 

Yes

37

Morales M, Hein K, Vogel Z. (2008) Hippocampal interneurons co-express transcripts encoding the alpha7 nicotinic receptor subunit and the cannabinoid receptor 1. Neuroscience. 2008 Mar 3;152(1):70-81. http://www.ncbi.nlm.nih.gov/pubmed/18222041 

Table 1. Relative percentage of interneurons co-expressing alpha7 nACh and GAD mRNAs in the hippocampus and the DG in the population of alpha7 nACh mRNA expressing interneurons http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2574619/table/T1/ 

 

Yes

 

 

Table 2. Relative percentage of interneurons co-expressing ?7 nACh and CB1 mRNAs in the hippocampus and the DG http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2574619/table/T2/ 

 

Yes

 

 

Table 3. Relative percentage of interneurons co-expressing ?7 nACh mRNA and CCK immunoreactivity in the hippocampus and the DG http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2574619/table/T3/ 

 

Yes

38

Morozova TV, Anholt RR, Mackay TF. (2006) Transcriptional response to alcohol exposure in Drosophila melanogaster. Genome Biol. 2006;7(10):R95. Epub 2006 Oct 20. http://www.ncbi.nlm.nih.gov/pubmed/17054780

Additional data file 2. List of all probe sets differentially expressed between treatment groups with q < 0.05. http://genomebiology.com/2006/7/10/R95#sec5

 

Yes

 

 

Table 1. Probe sets with altered transcriptional regulation after ethanol exposure with q < 0.001 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794562/table/T1/

 

Yes

39

Novikova SI, He F, Bai J, Badan I, Lidow IA, Lidow MS. (2005) Cocaine-induced changes in the expression of apoptosis-related genes in the fetal mouse cerebral wall. Neurotoxicol Teratol. 2005 Jan-Feb;27(1):3-14. http://www.ncbi.nlm.nih.gov/pubmed/15681117 

Table 1. Apoptosis-related genes affected in the frontal and occipital regions of the fetal mouse cerebral wall by chronic cocaine exposure

 

Yes

40

Paletzki RF, Myakishev MV, Polesskaya O, Orosz A, Hyman SE, Vinson C. (2008) Inhibiting activator protein-1 activity alters cocaine-induced gene expression and potentiates sensitization.  Neuroscience. 2008 Apr 9;152(4):1040-53. Epub 2008 Feb 7. http://www.ncbi.nlm.nih.gov/pubmed/18355967 

Table 1 List of genes differentially expressed in A-FOS expressing animals 24 hours after cocaine. The table includes the Affymetrix probe set ID for each gene along with its official gene symbol and description/function taken from the NCBI Entrez gene databases(more ...)

 

Yes

 

 

Table 2. Confirmation of a random sample of genes identified by microarrays as differentially expressed. 10 genes from the A-FOS regulated gene list and 6 genes from the cocaine regulated gene list were randomly picked and qPCR used to confirm their differential(more ...)

 

Yes

41

Perrotti LI, Weaver RR, Robison B, Renthal W, Maze I, Yazdani S, Elmore RG, Knapp DJ, Selley DE, Martin BR, Sim-Selley L, Bachtell RK, Self DW, Nestler EJ. (2008) Distinct patterns of DeltaFosB induction in brain by drugs of abuse.  Synapse. 62(5):358-69. http://www.ncbi.nlm.nih.gov/pubmed/18293355 

Table I Induction of DeltaFosB in brain by drugs of abuse.

 

Yes

42

Ren Y, Whittard J, Higuera-Matas A, Morris CV, Hurd YL. (2009) Cannabidiol, a nonpsychotropic component of cannabis, inhibits cue-induced heroin seeking and normalizes discrete mesolimbic neuronal disturbances.  J Neurosci. 29(47):14764-9. http://www.ncbi.nlm.nih.gov/pubmed/19940171

Table 1. Effects of CBD [5 mg/kg; after 24 hr (1X) or two weeks after the last day of repeated (three daily, 3X) injections] or vehicle treatment on the expression of CB1R mRNA and GluR1 protein level in subregions of the dorsal striatum (caudate-putamen) of animals following the cue-induced reinstatement session. http://www3.interscience.wiley.com/cgi-bin/fulltext/104084095/PDFSTART 

Supplemental Data

Yes

 

 

Table 2. Effects of CBD treatment (5 mg/kg) on the expression of CB1R mRNA level in subregions of the nucleus accumbens (NAc) and dorsal striatum (caudate-putamen) after 24 hr (1x) or two weeks after the last day of repeated (three daily, 3x) injections. http://www3.interscience.wiley.com/cgi-bin/fulltext/104084095/PDFSTART 

Supplemental Data

Yes

43

Renthal W, Maze I, Krishnan V, Covington HE 3rd, Xiao G, Kumar A, Russo SJ, Graham A, Tsankova N, Kippin TE, Kerstetter KA, Neve RL, Haggarty SJ, McKinsey TA, Bassel-Duby R, Olson EN, Nestler EJ. (2007) Histone Deacetylase 5 Epigenetically Controls Behavioral Adaptations to Chronic Emotional Stimuli Neuron. 2007 Nov 8;56(3):517-29. http://www.ncbi.nlm.nih.gov/pubmed/17988634

Table S2: List of Cocaine-Treated HDAC5 KO vs. Cocaine-Treated WT Significantly Regulated Genes (PDF 179 kb)

(Other Ranthal et al out of order #32)

Yes

 

 

Table S3: List of Cocaine-Treated HDAC5 KO vs. Saline-Treated HDAC5 KO Significantly Regulated Genes (PDF 184 kb)

http://www.cell.com/neuron/supplemental/S0896-6273%2807%2900766-0

Yes

 

 

Table S4: List of Saline-Treated HDAC5 KO vs. Saline-Treated WT Significantly Regulated Genes (PDF 173 kb)

http://www.cell.com/neuron/supplemental/S0896-6273%2807%2900766-0

Yes

 

 

Table S5: List of Cocaine-Treated WT vs. Saline-Treated WT Significantly Regulated Genes (PDF 175 kb)

http://www.cell.com/neuron/supplemental/S0896-6273%2807%2900766-0

Yes

44

Salas R, Main A, Gangitano DA, Zimmerman G, Ben-Ari S, Soreq H, De Biasi M. (2008) Nicotine relieves anxiogenic-like behavior in mice that overexpress the read-through variant of acetylcholinesterase but not in wild-type mice.  Mol Pharmacol. 2008 Dec;74(6):1641-8. Epub 2008 Sep 5.  http://www.ncbi.nlm.nih.gov/pubmed/18776044

TABLE 1  Differentially expressed genes in the TgR striatum http://molpharm.aspetjournals.org/content/74/6/1641/T1.expansion.html 

 

Yes

 

 

TABLE 3 Key cholinergic genes differentially expressed in the striatum of TgR mice
Shown genes were differentially regulated in the striatum of TgR mice as revealed by RT-PCR. Significantly changed genes (P < 0.05) are in boldface type. http://molpharm.aspetjournals.org/content/74/6/1641/T3.expansion.html 

 

Yes

45

Sharf R, Sarhan M, Dileone RJ. (2008) Orexin mediates the expression of precipitated morphine withdrawal and concurrent activation of the nucleus accumbens shell.  Biol Psychiatry. 2008 Aug 1;64(3):175-83. Epub 2008 Apr 18. http://www.ncbi.nlm.nih.gov/pubmed/18423425 

Table 1 Cell counts for immunohistochemical quantification are indicated. (A) The average number of counted orexin-positive cells, c-Fos positive cells, and the percentage of TH-positive cells double-labeled with c-Fos in the LH. (B) The average number of counted(more ...)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2529153/table/T1/ 

 

Yes

46

Shaw-Lutchman TZ, Barrot M, Wallace T, Gilden L, Zachariou V, Impey S, Duman RS, Storm D, Nestler EJ. (2002) Regional and cellular mapping of cAMP response element-mediated transcription during naltrexone-precipitated morphine withdrawal. J Neurosci. 22(9):3663-72. http://www.ncbi.nlm.nih.gov/pubmed/11978842

Table 2. Regulation of CRE-mediated transcription in brain by chronic morphine, naltrexone, and morphine withdrawal
http://www.jneurosci.org/cgi/content-nw/full/22/9/3663/T2

 

Yes

47

Soderman AR, Unterwald EM. (2008) Cocaine reward and hyperactivity in the rat: sites of mu opioid receptor modulation. Neuroscience. 2008 Jul 17;154(4):1506-16. Epub 2008 May 3. http://www.ncbi.nlm.nih.gov/sites/pubmed/18550291

Figure 5. Data are expressed as mean (+ / -SD) of cFos positive nuclei per brain region. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2585317/figure/F5/

 

Yes

 

 

Table 1. Data are expressed as mean (+ / - SD) of cFos positive nuclei 90 minutes following the test for expression of cocaine-induced conditioned place preference. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2585317/table/T1/

 

Yes

48

Sokolov BP, Jiang L, Trivedi NS, Aston C. (2003) Transcription profiling reveals mitochondrial, ubiquitin and signaling systems abnormalities in postmortem brains from subjects with a history of alcohol abuse or dependence.  J Neurosci Res. 2003 Jun 15;72(6):756-67. http://www.ncbi.nlm.nih.gov/pubmed/12774316

Table II. Genes with Altered Expression in Subjects With a History of Alcohol Abuse/Dependence
http://www3.interscience.wiley.com/cgi-bin/fulltext/104528507/HTMLSTART

 

Yes

49

Winstanley CA, LaPlant Q, Theobald DE, Green TA, Bachtell RK, Perrotti LI, DiLeone RJ, Russo SJ, Garth WJ, Self DW, Nestler EJ. (2007) DeltaFosB induction in orbitofrontal cortex mediates tolerance to cocaine-induced cognitive dysfunction. J Neurosci. 27(39):10497-507. http://www.ncbi.nlm.nih.gov/pubmed/17898221

supplemental material -Supplemental Table S2 :Cocaine regulation of gene expression in the OFC: Effects of deltaFosB and deltaJunD
Table S2a. Genes Significantly Regulated by Chronic Cocaine
Table S2b. Genes Significantly Regulated by deltaFosB

 

Yes

50

Yu L, Haverty PM, Mariani J, Wang Y, Shen HY, Schwarzschild MA, Weng Z, Chen JF. (2005) Genetic and pharmacological inactivation of adenosine A2A receptor reveals an Egr-2-mediated transcriptional regulatory network in the mouse striatum. Physiol Genomics. 2005 Sep 21;23(1):89-102. Epub 2005 Jul 26. http://www.ncbi.nlm.nih.gov/sites/pubmed/16046619

Table 1. Comparison of striatal gene expression by microarray and qPCR analyses http://physiolgenomics.physiology.org/cgi/content-nw/full/23/1/89/T1

 

Yes

 

 

Table 2. Comparative analysis of striatal gene expression regulated by A2AR KO and the A2AR antagonist SCH http://physiolgenomics.physiology.org/cgi/content-nw/full/23/1/89/T2

 

Yes

51

Yuferov V, Kroslak T, Laforge KS, Zhou Y, Ho A, Kreek MJ. (2003) Differential gene expression in the rat caudate putamen after binge cocaine administration: Advantage of triplicate microarray analysis  Synapse. 48(4):157-69.http://www.ncbi.nlm.nih.gov/pubmed/12687634

TABLE IV . Partial list of cocaine-regulated genes in the rat caudate putamen  http://www3.interscience.wiley.com/cgi-bin/fulltext/104084095/PDFSTART 

 

Yes

52

Zachariou V, Liu R, LaPlant Q, Xiao G, Renthal W, Chan GC, Storm DR, Aghajanian G, Nestler EJ. (2008) Distinct roles of adenylyl cyclases 1 and 8 in opiate dependence: behavioral, electrophysiological, and molecular studies. Biol Psychiatry. 63(11):1013-21. Epub 2008 Jan 28. http://www.ncbi.nlm.nih.gov/pubmed/18222416

Supplemental Table S1. Morphine regulation of gene expression in the LC in WT, AC1 KO, and AC8 KO Click here to view

 

Yes

 

 

Supplemental Table S2. Baseline regulation of gene expression in the LC Click here to view.

 

Yes

53

Zhang D, Zhang L, Tang Y, Zhang Q, Lou D, Sharp FR, Zhang J, Xu M. (2005) Repeated cocaine administration induces gene expression changes through the dopamine D1 receptors.  Neuropsychopharmacology. 30(8):1443-54. http://www.ncbi.nlm.nih.gov/pubmed/15770241 

Supplemental Table 1 (xls 48K)

 

Yes

 

 

Supplemental Table 2 (xls 130K)

 

Yes

54

Zombeck JA, Lewicki AD, Patel K, Gupta T, Rhodes JS. (2010) Patterns of neural activity associated with differential acute locomotor stimulation to cocaine and methamphetamine in adolescent versus adult male C57BL/6J mice. Neuroscience. 2010 Feb 17;165(4):1087-99. Epub 2009 Nov 22. http://www.ncbi.nlm.nih.gov/sites/pubmed/19932887

Table 1. Mean number of Fos positive cells and associated statistics after saline, 15 or 30 mg/kg cocaine

 

Yes

 

 

Table 2. The difference in cocaine-induced Fos between adolescents and adults after correcting for locomotor activity

 

Yes

 

 

Table 3. Mean number of Fos positive cells and associated statistics after saline, 2, or 4 mg/kg methamphetamine

 

Yes

 

 

Table 4. The difference in methamphetamine-induced Fos between adolescents and adults after correcting for locomotor activity

 

Yes

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