CHIP from tissue?# Biology - 生物学
m*t
1 楼
is it possible to do CHIP using tissue?
it seems all CHIP uses cells.
it seems all CHIP uses cells.
G*e
2 楼
Nature 457, 854-858 (12 February 2009) | doi:10.1038/nature07730; Received
16 October 2008; Accepted 18 December 2008
ChIP-seq accurately predicts tissue-specific activity of enhancers
Axel Visel1,4, Matthew J. Blow1,2,4, Zirong Li3, Tao Zhang2, Jennifer A.
Akiyama1, Amy Holt1, Ingrid Plajzer-Frick1, Malak Shoukry1, Crystal Wright2,
Feng Chen2, Veena Afzal1, Bing Ren3, Edward M. Rubin1,2 & Len A.
Pennacchio1,2
Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory,
Berkeley, California 94720, USA
US Department of Energy Joint Genome Institute, Walnut Creek, California
94598, USA
Ludwig Institute for Cancer Research, University of California San Diego
(UCSD) School of Medicine, La Jolla, California 92093, USA
These authors contributed equally to this work.
Correspondence to: Len A. Pennacchio1,2 Correspondence and requests for
materials should be addressed to L.A.P. (Email: L**********[email protected]).
Top of page
Abstract
A major yet unresolved quest in decoding the human genome is the
identification of the regulatory sequences that control the spatial and
temporal expression of genes. Distant-acting transcriptional enhancers are
particularly challenging to uncover because they are scattered among the
vast non-coding portion of the genome. Evolutionary sequence constraint can
facilitate the discovery of enhancers, but fails to predict when and where
they are active in vivo. Here we present the results of chromatin
immunoprecipitation with the enhancer-associated protein p300 followed by
massively parallel sequencing, and map several thousand in vivo binding
sites of p300 in mouse embryonic forebrain, midbrain and limb tissue. We
tested 86 of these sequences in a transgenic mouse assay, which in nearly
all cases demonstrated reproducible enhancer activity in the tissues that
were predicted by p300 binding. Our results indicate that in vivo mapping of
p300 binding is a highly accurate means for identifying enhancers and their
associated activities, and suggest that such data sets will be useful to
study the role of tissue-specific enhancers in human biology and disease on
a genome-wide scale.
16 October 2008; Accepted 18 December 2008
ChIP-seq accurately predicts tissue-specific activity of enhancers
Axel Visel1,4, Matthew J. Blow1,2,4, Zirong Li3, Tao Zhang2, Jennifer A.
Akiyama1, Amy Holt1, Ingrid Plajzer-Frick1, Malak Shoukry1, Crystal Wright2,
Feng Chen2, Veena Afzal1, Bing Ren3, Edward M. Rubin1,2 & Len A.
Pennacchio1,2
Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory,
Berkeley, California 94720, USA
US Department of Energy Joint Genome Institute, Walnut Creek, California
94598, USA
Ludwig Institute for Cancer Research, University of California San Diego
(UCSD) School of Medicine, La Jolla, California 92093, USA
These authors contributed equally to this work.
Correspondence to: Len A. Pennacchio1,2 Correspondence and requests for
materials should be addressed to L.A.P. (Email: L**********[email protected]).
Top of page
Abstract
A major yet unresolved quest in decoding the human genome is the
identification of the regulatory sequences that control the spatial and
temporal expression of genes. Distant-acting transcriptional enhancers are
particularly challenging to uncover because they are scattered among the
vast non-coding portion of the genome. Evolutionary sequence constraint can
facilitate the discovery of enhancers, but fails to predict when and where
they are active in vivo. Here we present the results of chromatin
immunoprecipitation with the enhancer-associated protein p300 followed by
massively parallel sequencing, and map several thousand in vivo binding
sites of p300 in mouse embryonic forebrain, midbrain and limb tissue. We
tested 86 of these sequences in a transgenic mouse assay, which in nearly
all cases demonstrated reproducible enhancer activity in the tissues that
were predicted by p300 binding. Our results indicate that in vivo mapping of
p300 binding is a highly accurate means for identifying enhancers and their
associated activities, and suggest that such data sets will be useful to
study the role of tissue-specific enhancers in human biology and disease on
a genome-wide scale.
w*r
3 楼
之前查过，
很多ChIP是用embryo做的，也有用liver的。都比较嫩，把组织研磨一下基本就可以当
cell用了。
后来我们做muscle的ChIP，比较结实，发现磨半天也磨不碎。。。
后来我就拿剪子狂剪，剪成很细碎的小块，固定15分钟，固定完了用PBS洗洗，放在
lysis buffer里洗洗，匀浆。ChIP-Seq的结果很好
很多ChIP是用embryo做的，也有用liver的。都比较嫩，把组织研磨一下基本就可以当
cell用了。
后来我们做muscle的ChIP，比较结实，发现磨半天也磨不碎。。。
后来我就拿剪子狂剪，剪成很细碎的小块，固定15分钟，固定完了用PBS洗洗，放在
lysis buffer里洗洗，匀浆。ChIP-Seq的结果很好
m*l
4 楼
用液氮粉碎。
E*2
5 楼
如果是做histone的话，可以用MNase,做native chip
E*2
6 楼
如果是做histone的话，可以用MNase,做native chip
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