-
1
-
-
79951694175
-
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
-
Aird, D., Ross, M.G., Chen, W.S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D.B., Nusbaum, C. & Gnirke, A. (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12, R18.
-
(2011)
Genome Biol
, vol.12
, pp. R18
-
-
Aird, D.1
Ross, M.G.2
Chen, W.S.3
Danielsson, M.4
Fennell, T.5
Russ, C.6
Jaffe, D.B.7
Nusbaum, C.8
Gnirke, A.9
-
2
-
-
77957984028
-
DNA methylation regulates cocaine-induced behavioral sensitization in mice
-
Anier, K., Malinovskaja, K., Aonurm-Helm, A., Zharkovsky, A. & Kalda, A. (2010) DNA methylation regulates cocaine-induced behavioral sensitization in mice. Neuropsychopharmacology 35, 2450-2461.
-
(2010)
Neuropsychopharmacology
, vol.35
, pp. 2450-2461
-
-
Anier, K.1
Malinovskaja, K.2
Aonurm-Helm, A.3
Zharkovsky, A.4
Kalda, A.5
-
3
-
-
84866860120
-
Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling
-
Boyle, P., Clement, K., Gu, H., Smith, Z.D., Ziller, M., Fostel, J.L., Holmes, L., Meldrim, J., Kelley, F., Gnirke, A. & Meissner, A. (2012) Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol 13, R92.
-
(2012)
Genome Biol
, vol.13
, pp. R92
-
-
Boyle, P.1
Clement, K.2
Gu, H.3
Smith, Z.D.4
Ziller, M.5
Fostel, J.L.6
Holmes, L.7
Meldrim, J.8
Kelley, F.9
Gnirke, A.10
Meissner, A.11
-
4
-
-
84862640477
-
Maternal deprivation in rats is associated with corticotropin releasing hormone (Crh) promoter hypomethylation and enhances Crh transcriptional responses to stress in adulthood
-
Chen, J., Evans, A.N., Liu, Y., Honda, M., Saavedra, J.M. & Aguilera, G. (2012) Maternal deprivation in rats is associated with corticotropin releasing hormone (Crh) promoter hypomethylation and enhances Crh transcriptional responses to stress in adulthood. J Neuroendocrinol 24, 1055-1064.
-
(2012)
J Neuroendocrinol
, vol.24
, pp. 1055-1064
-
-
Chen, J.1
Evans, A.N.2
Liu, Y.3
Honda, M.4
Saavedra, J.M.5
Aguilera, G.6
-
5
-
-
84867539515
-
Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus
-
Cowley, M., Wood, A.J., Bohm, S., Schulz, R. & Oakey, R.J. (2012) Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. Nucleic Acids Res 40, 8917-8926.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 8917-8926
-
-
Cowley, M.1
Wood, A.J.2
Bohm, S.3
Schulz, R.4
Oakey, R.J.5
-
6
-
-
84884901586
-
DNA methylation regulates associative reward learning
-
Day, J.J., Childs, D., Guzman-Karlsson, M.C., Kibe, M., Moulden, J., Song, E., Tahir, A. & Sweatt, J.D. (2013) DNA methylation regulates associative reward learning. Nat Neurosci 16, 1445-1452.
-
(2013)
Nat Neurosci
, vol.16
, pp. 1445-1452
-
-
Day, J.J.1
Childs, D.2
Guzman-Karlsson, M.C.3
Kibe, M.4
Moulden, J.5
Song, E.6
Tahir, A.7
Sweatt, J.D.8
-
7
-
-
84875010066
-
Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing
-
De Meyer, T., Mampaey, E., Vlemmix, M., Denil, S., Trooskens, G., Renard, J.P., De Keulenaer, S., Dehan, P., Menschaert, G. & Van Criekinge, W. (2013) Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing. PLoS One 8, e59068.
-
(2013)
PLoS One
, vol.8
, pp. e59068
-
-
De Meyer, T.1
Mampaey, E.2
Vlemmix, M.3
Denil, S.4
Trooskens, G.5
Renard, J.P.6
De Keulenaer, S.7
Dehan, P.8
Menschaert, G.9
Van Criekinge, W.10
-
9
-
-
21544433777
-
Reelin promoter hypermethylation in schizophrenia
-
Grayson, D.R., Jia, X., Chen, Y., Sharma, R.P., Mitchell, C.P., Guidotti, A. & Costa, E. (2005) Reelin promoter hypermethylation in schizophrenia. Proc Natl Acad Sci U S A 102, 9341-9346.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 9341-9346
-
-
Grayson, D.R.1
Jia, X.2
Chen, Y.3
Sharma, R.P.4
Mitchell, C.P.5
Guidotti, A.6
Costa, E.7
-
10
-
-
79952788617
-
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
-
Gu, H., Smith, Z.D., Bock, C., Boyle, P., Gnirke, A. & Meissner, A. (2011) Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 6, 468-481.
-
(2011)
Nat Protoc
, vol.6
, pp. 468-481
-
-
Gu, H.1
Smith, Z.D.2
Bock, C.3
Boyle, P.4
Gnirke, A.5
Meissner, A.6
-
11
-
-
81555204354
-
FACS purification of immunolabeled cell types from adult rat brain
-
Guez-Barber, D., Fanous, S., Harvey, B.K., Zhang, Y., Lehrmann, E., Becker, K.G., Picciotto, M.R. & Hope, B.T. (2012) FACS purification of immunolabeled cell types from adult rat brain. J Neurosci Methods 203, 10-18.
-
(2012)
J Neurosci Methods
, vol.203
, pp. 10-18
-
-
Guez-Barber, D.1
Fanous, S.2
Harvey, B.K.3
Zhang, Y.4
Lehrmann, E.5
Becker, K.G.6
Picciotto, M.R.7
Hope, B.T.8
-
12
-
-
84875700729
-
A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression
-
Guintivano, J., Aryee, M.J. & Kaminsky, Z.A. (2013) A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression. Epigenetics 8, 290-302.
-
(2013)
Epigenetics
, vol.8
, pp. 290-302
-
-
Guintivano, J.1
Aryee, M.J.2
Kaminsky, Z.A.3
-
13
-
-
80053270332
-
Neuronal activity modifies the DNA methylation landscape in the adult brain
-
Guo, J.U., Ma, D.K., Mo, H., Ball, M.P., Jang, M.H., Bonaguidi, M.A., Balazer, J.A., Eaves, H.L., Xie, B., Ford, E., Zhang, K., Ming, G.L., Gao, Y. & Song, H. (2011) Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci 14, 1345-1351.
-
(2011)
Nat Neurosci
, vol.14
, pp. 1345-1351
-
-
Guo, J.U.1
Ma, D.K.2
Mo, H.3
Ball, M.P.4
Jang, M.H.5
Bonaguidi, M.A.6
Balazer, J.A.7
Eaves, H.L.8
Xie, B.9
Ford, E.10
Zhang, K.11
Ming, G.L.12
Gao, Y.13
Song, H.14
-
14
-
-
84893740377
-
Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain
-
Guo, J.U., Su, Y., Shin, J.H., Shin, J., Li, H., Xie, B., Zhong, C., Hu, S., Le, T., Fan, G., Zhu, H., Chang, Q., Gao, Y., Ming, G.L. & Song, H. (2013) Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat Neurosci 17, 215-222.
-
(2013)
Nat Neurosci
, vol.17
, pp. 215-222
-
-
Guo, J.U.1
Su, Y.2
Shin, J.H.3
Shin, J.4
Li, H.5
Xie, B.6
Zhong, C.7
Hu, S.8
Le, T.9
Fan, G.10
Zhu, H.11
Chang, Q.12
Gao, Y.13
Ming, G.L.14
Song, H.15
-
15
-
-
84858681550
-
Commentary: the seven plagues of epigenetic epidemiology
-
Heijmans, B.T. & Mill, J. (2012) Commentary: the seven plagues of epigenetic epidemiology. Int J Epidemiol 41, 74-78.
-
(2012)
Int J Epidemiol
, vol.41
, pp. 74-78
-
-
Heijmans, B.T.1
Mill, J.2
-
16
-
-
84861547680
-
Evidence that microglia mediate the neurobiological effects of chronic psychological stress on the medial prefrontal cortex
-
Hinwood, M., Morandini, J., Day, T.A. & Walker, F.R. (2012) Evidence that microglia mediate the neurobiological effects of chronic psychological stress on the medial prefrontal cortex. Cereb Cortex 22, 1442-1454.
-
(2012)
Cereb Cortex
, vol.22
, pp. 1442-1454
-
-
Hinwood, M.1
Morandini, J.2
Day, T.A.3
Walker, F.R.4
-
17
-
-
79955557706
-
Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons
-
Iwamoto, K., Bundo, M., Ueda, J., Oldham, M.C., Ukai, W., Hashimoto, E., Saito, T., Geschwind, D.H. & Kato, T. (2011) Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons. Genome Res 21, 688-696.
-
(2011)
Genome Res
, vol.21
, pp. 688-696
-
-
Iwamoto, K.1
Bundo, M.2
Ueda, J.3
Oldham, M.C.4
Ukai, W.5
Hashimoto, E.6
Saito, T.7
Geschwind, D.H.8
Kato, T.9
-
18
-
-
43549109877
-
Isolation of neuronal chromatin from brain tissue
-
Jiang, Y., Matevossian, A., Huang, H.S., Straubhaar, J. & Akbarian, S. (2008) Isolation of neuronal chromatin from brain tissue. BMC Neurosci 9, 42.
-
(2008)
BMC Neurosci
, vol.9
, pp. 42
-
-
Jiang, Y.1
Matevossian, A.2
Huang, H.S.3
Straubhaar, J.4
Akbarian, S.5
-
19
-
-
84885476091
-
BDNF promoter methylation and suicidal behavior in depressive patients
-
Kang, H.J., Kim, J.M., Lee, J.Y., Kim, S.Y., Bae, K.Y., Kim, S.W., Shin, I.S., Kim, H.R., Shin, M.G. & Yoon, J.S. (2013) BDNF promoter methylation and suicidal behavior in depressive patients. J Affect Disord 151, 679-685.
-
(2013)
J Affect Disord
, vol.151
, pp. 679-685
-
-
Kang, H.J.1
Kim, J.M.2
Lee, J.Y.3
Kim, S.Y.4
Bae, K.Y.5
Kim, S.W.6
Shin, I.S.7
Kim, H.R.8
Shin, M.G.9
Yoon, J.S.10
-
20
-
-
33744938449
-
LUMA (LUminometric methylation assay) - a high throughput method to the analysis of genomic DNA methylation
-
Karimi, M., Johansson, S., Stach, D., Corcoran, M., Grander, D., Schalling, M., Bakalkin, G., Lyko, F., Larsson, C. & Ekstrom, T.J. (2006) LUMA (LUminometric methylation assay) - a high throughput method to the analysis of genomic DNA methylation. Exp Cell Res 312, 1989-1995.
-
(2006)
Exp Cell Res
, vol.312
, pp. 1989-1995
-
-
Karimi, M.1
Johansson, S.2
Stach, D.3
Corcoran, M.4
Grander, D.5
Schalling, M.6
Bakalkin, G.7
Lyko, F.8
Larsson, C.9
Ekstrom, T.J.10
-
21
-
-
84891766375
-
Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites
-
Kozlenkov, A., Roussos, P., Timashpolsky, A., Barbu, M., Rudchenko, S., Bibikova, M., Klotzle, B., Byne, W., Lyddon, R., Di Narzo, A.F., Hurd, Y.L., Koonin, E.V. & Dracheva, S. (2013) Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites. Nucleic Acids Res 42, 109-127.
-
(2013)
Nucleic Acids Res
, vol.42
, pp. 109-127
-
-
Kozlenkov, A.1
Roussos, P.2
Timashpolsky, A.3
Barbu, M.4
Rudchenko, S.5
Bibikova, M.6
Klotzle, B.7
Byne, W.8
Lyddon, R.9
Di Narzo, A.F.10
Hurd, Y.L.11
Koonin, E.V.12
Dracheva, S.13
-
22
-
-
84855300158
-
Genome-wide epigenetic regulation by early-life trauma
-
Labonte, B., Suderman, M., Maussion, G., Navaro, L., Yerko, V., Mahar, I., Bureau, A., Mechawar, N., Szyf, M., Meaney, M.J. & Turecki, G. (2012) Genome-wide epigenetic regulation by early-life trauma. Arch Gen Psychiatry 69, 722-731.
-
(2012)
Arch Gen Psychiatry
, vol.69
, pp. 722-731
-
-
Labonte, B.1
Suderman, M.2
Maussion, G.3
Navaro, L.4
Yerko, V.5
Mahar, I.6
Bureau, A.7
Mechawar, N.8
Szyf, M.9
Meaney, M.J.10
Turecki, G.11
-
23
-
-
84879439091
-
Genome-wide methylation changes in the brains of suicide completers
-
Labonte, B., Suderman, M., Maussion, G., Lopez, J.P., Navarro-Sanchez, L., Yerko, V., Mechawar, N., Szyf, M., Meaney, M.J. & Turecki, G. (2013) Genome-wide methylation changes in the brains of suicide completers. Am J Psychiatry 170, 511-520.
-
(2013)
Am J Psychiatry
, vol.170
, pp. 511-520
-
-
Labonte, B.1
Suderman, M.2
Maussion, G.3
Lopez, J.P.4
Navarro-Sanchez, L.5
Yerko, V.6
Mechawar, N.7
Szyf, M.8
Meaney, M.J.9
Turecki, G.10
-
24
-
-
84880011207
-
Long-lasting alterations to DNA methylation and ncRNAs could underlie the effects of fetal alcohol exposure in mice
-
Laufer, B.I., Mantha, K., Kleiber, M.L., Diehl, E.J., Addison, S.M. & Singh, S.M. (2013) Long-lasting alterations to DNA methylation and ncRNAs could underlie the effects of fetal alcohol exposure in mice. Dis Model Mech 6, 977-992.
-
(2013)
Dis Model Mech
, vol.6
, pp. 977-992
-
-
Laufer, B.I.1
Mantha, K.2
Kleiber, M.L.3
Diehl, E.J.4
Addison, S.M.5
Singh, S.M.6
-
25
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. & Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
26
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. & Durbin, R. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
27
-
-
84894359441
-
Major epigenetic development distinguishing neuronal and non-neuronal cells occurs postnatally in the murine hypothalamus
-
Li, G., Zhang, W., Baker, M.S., Laritsky, E., Mattan-Hung, N., Yu, D., Kunde-Ramamoorthy, G., Simerly, R.B., Chen, R., Shen, L. & Waterland, R.A. (2013) Major epigenetic development distinguishing neuronal and non-neuronal cells occurs postnatally in the murine hypothalamus. Hum Mol Genet 23, 1579-1590.
-
(2013)
Hum Mol Genet
, vol.23
, pp. 1579-1590
-
-
Li, G.1
Zhang, W.2
Baker, M.S.3
Laritsky, E.4
Mattan-Hung, N.5
Yu, D.6
Kunde-Ramamoorthy, G.7
Simerly, R.B.8
Chen, R.9
Shen, L.10
Waterland, R.A.11
-
28
-
-
84879663784
-
Global epigenomic reconfiguration during mammalian brain development
-
Lister, R., Mukamel, E.A., Nery, J.R. et al. (2013) Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905.
-
(2013)
Science
, vol.341
, pp. 1237905
-
-
Lister, R.1
Mukamel, E.A.2
Nery, J.R.3
-
29
-
-
33344470365
-
FACS-array profiling of striatal projection neuron subtypes in juvenile and adult mouse brains
-
Lobo, M.K., Karsten, S.L., Gray, M., Geschwind, D.H. & Yang, X.W. (2006) FACS-array profiling of striatal projection neuron subtypes in juvenile and adult mouse brains. Nat Neurosci 9, 443-452.
-
(2006)
Nat Neurosci
, vol.9
, pp. 443-452
-
-
Lobo, M.K.1
Karsten, S.L.2
Gray, M.3
Geschwind, D.H.4
Yang, X.W.5
-
30
-
-
84875221641
-
Epigenetic modifications of GABAergic interneurons are associated with the schizophrenia-like phenotype induced by prenatal stress in mice
-
Matrisciano, F., Tueting, P., Dalal, I., Kadriu, B., Grayson, D.R., Davis, J.M., Nicoletti, F. & Guidotti, A. (2013) Epigenetic modifications of GABAergic interneurons are associated with the schizophrenia-like phenotype induced by prenatal stress in mice. Neuropharmacology 68, 184-194.
-
(2013)
Neuropharmacology
, vol.68
, pp. 184-194
-
-
Matrisciano, F.1
Tueting, P.2
Dalal, I.3
Kadriu, B.4
Grayson, D.R.5
Davis, J.M.6
Nicoletti, F.7
Guidotti, A.8
-
31
-
-
84884828422
-
Recommendations for the design and analysis of epigenome-wide association studies
-
Michels, K.B., Binder, A.M., Dedeurwaerder, S., Epstein, C.B., Greally, J.M., Gut, I., Houseman, E.A., Izzi, B., Kelsey, K.T., Meissner, A., Milosavljevic, A., Siegmund, K.D., Bock, C. & Irizarry, R.A. (2013) Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods 10, 949-955.
-
(2013)
Nat Methods
, vol.10
, pp. 949-955
-
-
Michels, K.B.1
Binder, A.M.2
Dedeurwaerder, S.3
Epstein, C.B.4
Greally, J.M.5
Gut, I.6
Houseman, E.A.7
Izzi, B.8
Kelsey, K.T.9
Meissner, A.10
Milosavljevic, A.11
Siegmund, K.D.12
Bock, C.13
Irizarry, R.A.14
-
32
-
-
41149140859
-
Epigenomic profiling reveals DNA-methylation changes associated with major psychosis
-
Mill, J., Tang, T., Kaminsky, Z., Khare, T., Yazdanpanah, S., Bouchard, L., Jia, P., Assadzadeh, A., Flanagan, J., Schumacher, A., Wang, S.C. & Petronis, A. (2008) Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 82, 696-711.
-
(2008)
Am J Hum Genet
, vol.82
, pp. 696-711
-
-
Mill, J.1
Tang, T.2
Kaminsky, Z.3
Khare, T.4
Yazdanpanah, S.5
Bouchard, L.6
Jia, P.7
Assadzadeh, A.8
Flanagan, J.9
Schumacher, A.10
Wang, S.C.11
Petronis, A.12
-
33
-
-
33847614418
-
Covalent modification of DNA regulates memory formation
-
Miller, C.A. & Sweatt, J.D. (2007) Covalent modification of DNA regulates memory formation. Neuron 53, 857-869.
-
(2007)
Neuron
, vol.53
, pp. 857-869
-
-
Miller, C.A.1
Sweatt, J.D.2
-
34
-
-
77952886110
-
Cortical DNA methylation maintains remote memory
-
Miller, C.A., Gavin, C.F., White, J.A., Parrish, R.R., Honasoge, A., Yancey, C.R., Rivera, I.M., Rubio, M.D., Rumbaugh, G. & Sweatt, J.D. (2010) Cortical DNA methylation maintains remote memory. Nat Neurosci 13, 664-666.
-
(2010)
Nat Neurosci
, vol.13
, pp. 664-666
-
-
Miller, C.A.1
Gavin, C.F.2
White, J.A.3
Parrish, R.R.4
Honasoge, A.5
Yancey, C.R.6
Rivera, I.M.7
Rubio, M.D.8
Rumbaugh, G.9
Sweatt, J.D.10
-
35
-
-
84877111454
-
Widespread and extensive lengthening of 3′ UTRs in the mammalian brain
-
Miura, P., Shenker, S., Andreu-Agullo, C., Westholm, J.O. & Lai, E.C. (2013) Widespread and extensive lengthening of 3′ UTRs in the mammalian brain. Genome Res 23, 812-825.
-
(2013)
Genome Res
, vol.23
, pp. 812-825
-
-
Miura, P.1
Shenker, S.2
Andreu-Agullo, C.3
Westholm, J.O.4
Lai, E.C.5
-
36
-
-
84864127740
-
Long-lasting regulation of hippocampal Bdnf gene transcription after contextual fear conditioning
-
Mizuno, K., Dempster, E., Mill, J. & Giese, K.P. (2012) Long-lasting regulation of hippocampal Bdnf gene transcription after contextual fear conditioning. Genes Brain Behav 11, 651-659.
-
(2012)
Genes Brain Behav
, vol.11
, pp. 651-659
-
-
Mizuno, K.1
Dempster, E.2
Mill, J.3
Giese, K.P.4
-
37
-
-
70549104872
-
Dynamic DNA methylation programs persistent adverse effects of early-life stress
-
Murgatroyd, C., Patchev, A.V., Wu, Y., Micale, V., Bockmuhl, Y., Fischer, D., Holsboer, F., Wotjak, C.T., Almeida, O.F. & Spengler, D. (2009) Dynamic DNA methylation programs persistent adverse effects of early-life stress. Nat Neurosci 12, 1559-1566.
-
(2009)
Nat Neurosci
, vol.12
, pp. 1559-1566
-
-
Murgatroyd, C.1
Patchev, A.V.2
Wu, Y.3
Micale, V.4
Bockmuhl, Y.5
Fischer, D.6
Holsboer, F.7
Wotjak, C.T.8
Almeida, O.F.9
Spengler, D.10
-
38
-
-
77952240732
-
DNA methylation of the POMC gene promoter is associated with craving in alcohol dependence
-
Muschler, M.A., Hillemacher, T., Kraus, C., Kornhuber, J., Bleich, S. & Frieling, H. (2010) DNA methylation of the POMC gene promoter is associated with craving in alcohol dependence. J Neural Transm 117, 513-519.
-
(2010)
J Neural Transm
, vol.117
, pp. 513-519
-
-
Muschler, M.A.1
Hillemacher, T.2
Kraus, C.3
Kornhuber, J.4
Bleich, S.5
Frieling, H.6
-
39
-
-
78651251739
-
Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias
-
Nair, S.S., Coolen, M.W., Stirzaker, C., Song, J.Z., Statham, A.L., Strbenac, D., Robinson, M.D. & Clark, S.J. (2011) Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics 6, 34-44.
-
(2011)
Epigenetics
, vol.6
, pp. 34-44
-
-
Nair, S.S.1
Coolen, M.W.2
Stirzaker, C.3
Song, J.Z.4
Statham, A.L.5
Strbenac, D.6
Robinson, M.D.7
Clark, S.J.8
-
40
-
-
84871664677
-
Neuronal cell-type specific DNA methylation patterns of the Cacna1c gene
-
Nishioka, M., Shimada, T., Bundo, M., Ukai, W., Hashimoto, E., Saito, T., Kano, Y., Sasaki, T., Kasai, K., Kato, T. & Iwamoto, K. (2013) Neuronal cell-type specific DNA methylation patterns of the Cacna1c gene. Int J Dev Neurosci 31, 89-95.
-
(2013)
Int J Dev Neurosci
, vol.31
, pp. 89-95
-
-
Nishioka, M.1
Shimada, T.2
Bundo, M.3
Ukai, W.4
Hashimoto, E.5
Saito, T.6
Kano, Y.7
Sasaki, T.8
Kasai, K.9
Kato, T.10
Iwamoto, K.11
-
41
-
-
84880492025
-
Differential gene body methylation and reduced expression of cell adhesion and neurotransmitter receptor genes in adverse maternal environment
-
Oh, J.E., Chambwe, N., Klein, S., Gal, J., Andrews, S., Gleason, G., Shaknovich, R., Melnick, A., Campagne, F. & Toth, M. (2013) Differential gene body methylation and reduced expression of cell adhesion and neurotransmitter receptor genes in adverse maternal environment. Transl Psychiatry 3, e218.
-
(2013)
Transl Psychiatry
, vol.3
, pp. e218
-
-
Oh, J.E.1
Chambwe, N.2
Klein, S.3
Gal, J.4
Andrews, S.5
Gleason, G.6
Shaknovich, R.7
Melnick, A.8
Campagne, F.9
Toth, M.10
-
42
-
-
78649642465
-
Flow cytometric sorting of neuronal and glial nuclei from central nervous system tissue
-
Okada, S., Saiwai, H., Kumamaru, H., Kubota, K., Harada, A., Yamaguchi, M., Iwamoto, Y. & Ohkawa, Y. (2011) Flow cytometric sorting of neuronal and glial nuclei from central nervous system tissue. J Cell Physiol 226, 552-558.
-
(2011)
J Cell Physiol
, vol.226
, pp. 552-558
-
-
Okada, S.1
Saiwai, H.2
Kumamaru, H.3
Kubota, K.4
Harada, A.5
Yamaguchi, M.6
Iwamoto, Y.7
Ohkawa, Y.8
-
43
-
-
0015697938
-
Isolated removal of hypothalamic or other brain nuclei of the rat
-
Palkovits, M. (1973) Isolated removal of hypothalamic or other brain nuclei of the rat. Brain Res 59, 449-450.
-
(1973)
Brain Res
, vol.59
, pp. 449-450
-
-
Palkovits, M.1
-
44
-
-
78650058320
-
Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation
-
Robinson, M.D., Stirzaker, C., Statham, A.L., Coolen, M.W., Song, J.Z., Nair, S.S., Strbenac, D., Speed, T.P. & Clark, S.J. (2010) Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res 20, 1719-1729.
-
(2010)
Genome Res
, vol.20
, pp. 1719-1729
-
-
Robinson, M.D.1
Stirzaker, C.2
Statham, A.L.3
Coolen, M.W.4
Song, J.Z.5
Nair, S.S.6
Strbenac, D.7
Speed, T.P.8
Clark, S.J.9
-
45
-
-
84871768667
-
Genome-wide DNA methylation scan in major depressive disorder
-
Sabunciyan, S., Aryee, M.J., Irizarry, R.A., Rongione, M., Webster, M.J., Kaufman, W.E., Murakami, P., Lessard, A., Yolken, R.H., Feinberg, A.P. & Potash, J.B. (2012) Genome-wide DNA methylation scan in major depressive disorder. PLoS One 7, e34451.
-
(2012)
PLoS One
, vol.7
, pp. e34451
-
-
Sabunciyan, S.1
Aryee, M.J.2
Irizarry, R.A.3
Rongione, M.4
Webster, M.J.5
Kaufman, W.E.6
Murakami, P.7
Lessard, A.8
Yolken, R.H.9
Feinberg, A.P.10
Potash, J.B.11
-
46
-
-
84862163088
-
Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain
-
Saxena, A., Wagatsuma, A., Noro, Y., Kuji, T., Asaka-Oba, A., Watahiki, A., Gurnot, C., Fagiolini, M., Hensch, T.K. & Carninci, P. (2012) Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain. Biotechniques 52, 381-385.
-
(2012)
Biotechniques
, vol.52
, pp. 381-385
-
-
Saxena, A.1
Wagatsuma, A.2
Noro, Y.3
Kuji, T.4
Asaka-Oba, A.5
Watahiki, A.6
Gurnot, C.7
Fagiolini, M.8
Hensch, T.K.9
Carninci, P.10
-
47
-
-
84882452116
-
Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation
-
Schor, I.E., Fiszbein, A., Petrillo, E. & Kornblihtt, A.R. (2013) Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation. EMBO J 32, 2264-2274.
-
(2013)
EMBO J
, vol.32
, pp. 2264-2274
-
-
Schor, I.E.1
Fiszbein, A.2
Petrillo, E.3
Kornblihtt, A.R.4
-
48
-
-
84864277953
-
DNA methylation in the developing hippocampus and amygdala of anxiety-prone versus risk-taking rats
-
Simmons, R.K., Howard, J.L., Simpson, D.N., Akil, H. & Clinton, S.M. (2012) DNA methylation in the developing hippocampus and amygdala of anxiety-prone versus risk-taking rats. Dev Neurosci 34, 58-67.
-
(2012)
Dev Neurosci
, vol.34
, pp. 58-67
-
-
Simmons, R.K.1
Howard, J.L.2
Simpson, D.N.3
Akil, H.4
Clinton, S.M.5
-
49
-
-
84883719710
-
Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
-
Stevens, M., Cheng, J.B., Li, D., Xie, M., Hong, C., Maire, C.L., Ligon, K.L., Hirst, M., Marra, M.A., Costello, J.F. & Wang, T. (2013) Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods. Genome Res 23, 1541-1553.
-
(2013)
Genome Res
, vol.23
, pp. 1541-1553
-
-
Stevens, M.1
Cheng, J.B.2
Li, D.3
Xie, M.4
Hong, C.5
Maire, C.L.6
Ligon, K.L.7
Hirst, M.8
Marra, M.A.9
Costello, J.F.10
Wang, T.11
-
50
-
-
84858146301
-
Methylome analysis using MeDIP-seq with low DNA concentrations
-
Taiwo, O., Wilson, G.A., Morris, T., Seisenberger, S., Reik, W., Pearce, D., Beck, S. & Butcher, L.M. (2012) Methylome analysis using MeDIP-seq with low DNA concentrations. Nat Protoc 7, 617-636.
-
(2012)
Nat Protoc
, vol.7
, pp. 617-636
-
-
Taiwo, O.1
Wilson, G.A.2
Morris, T.3
Seisenberger, S.4
Reik, W.5
Pearce, D.6
Beck, S.7
Butcher, L.M.8
-
51
-
-
84863341417
-
Reversal of cocaine-conditioned place preference through methyl supplementation in mice: altering global DNA methylation in the prefrontal cortex
-
Tian, W., Zhao, M., Li, M., Song, T., Zhang, M., Quan, L., Li, S. & Sun, Z.S. (2012) Reversal of cocaine-conditioned place preference through methyl supplementation in mice: altering global DNA methylation in the prefrontal cortex. PLoS One 7, e33435.
-
(2012)
PLoS One
, vol.7
, pp. e33435
-
-
Tian, W.1
Zhao, M.2
Li, M.3
Song, T.4
Zhang, M.5
Quan, L.6
Li, S.7
Sun, Z.S.8
-
52
-
-
84874952864
-
Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes
-
Trimarchi, M.P., Murphy, M., Frankhouser, D., Rodriguez, B.A., Curfman, J., Marcucci, G., Yan, P. & Bundschuh, R. (2012) Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes. BMC Genomics 13 (Suppl 8), S6.
-
(2012)
BMC Genomics
, vol.13
, pp. S6
-
-
Trimarchi, M.P.1
Murphy, M.2
Frankhouser, D.3
Rodriguez, B.A.4
Curfman, J.5
Marcucci, G.6
Yan, P.7
Bundschuh, R.8
-
53
-
-
21544470472
-
Brain DNA methylation as an index of genome participation in mechanisms of individually acquired memory
-
Vanyushi, B.F., Tushmalo, N.A. & Guskova, L.V. (1974) Brain DNA methylation as an index of genome participation in mechanisms of individually acquired memory. Dok Akad Nauk SSSR 219, 742-744.
-
(1974)
Dok Akad Nauk SSSR
, vol.219
, pp. 742-744
-
-
Vanyushi, B.F.1
Tushmalo, N.A.2
Guskova, L.V.3
-
54
-
-
0036708169
-
Analysis of neuronal gene expression with laser capture microdissection
-
Vincent, V.A., DeVoss, J.J., Ryan, H.S. & Murphy, G.M. Jr. (2002) Analysis of neuronal gene expression with laser capture microdissection. J Neurosci Res 69, 578-586.
-
(2002)
J Neurosci Res
, vol.69
, pp. 578-586
-
-
Vincent, V.A.1
DeVoss, J.J.2
Ryan, H.S.3
Murphy Jr, G.M.4
-
55
-
-
84881298161
-
Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing
-
Wang, J., Xia, Y., Li, L., Gong, D., Yao, Y., Luo, H., Lu, H., Yi, N., Wu, H., Zhang, X., Tao, Q. & Gao, F. (2013) Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing. BMC Genomics 14, 11.
-
(2013)
BMC Genomics
, vol.14
, pp. 11
-
-
Wang, J.1
Xia, Y.2
Li, L.3
Gong, D.4
Yao, Y.5
Luo, H.6
Lu, H.7
Yi, N.8
Wu, H.9
Zhang, X.10
Tao, Q.11
Gao, F.12
-
56
-
-
0030697141
-
Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA
-
Warnecke, P.M., Stirzaker, C., Melki, J.R., Millar, D.S., Paul, C.L. & Clark, S.J. (1997) Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Res 25, 4422-4426.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 4422-4426
-
-
Warnecke, P.M.1
Stirzaker, C.2
Melki, J.R.3
Millar, D.S.4
Paul, C.L.5
Clark, S.J.6
-
57
-
-
3342989681
-
Epigenetic programming by maternal behavior
-
Weaver, I.C., Cervoni, N., Champagne, F.A., D'Alessio, A.C., Sharma, S., Seckl, J.R., Dymov, S., Szyf, M. & Meaney, M.J. (2004) Epigenetic programming by maternal behavior. Nat Neurosci 7, 847-854.
-
(2004)
Nat Neurosci
, vol.7
, pp. 847-854
-
-
Weaver, I.C.1
Cervoni, N.2
Champagne, F.A.3
D'Alessio, A.C.4
Sharma, S.5
Seckl, J.R.6
Dymov, S.7
Szyf, M.8
Meaney, M.J.9
-
58
-
-
43249087733
-
Regulation of alternative polyadenylation by genomic imprinting
-
Wood, A.J., Schulz, R., Woodfine, K., Koltowska, K., Beechey, C.V., Peters, J., Bourc'his, D. & Oakey, R.J. (2008) Regulation of alternative polyadenylation by genomic imprinting. Genes Dev 22, 1141-1146.
-
(2008)
Genes Dev
, vol.22
, pp. 1141-1146
-
-
Wood, A.J.1
Schulz, R.2
Woodfine, K.3
Koltowska, K.4
Beechey, C.V.5
Peters, J.6
Bourc'his, D.7
Oakey, R.J.8
-
59
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W. & Liu, X.S. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9, R137.
-
(2008)
Genome Biol
, vol.9
, pp. R137
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
Liu, X.S.11
|