d****i
发帖数: 2346 | 1 谢谢！nested PCR我知道，我去看看用这个有没有办法改善。 |
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c****e
发帖数: 188 | 2 I am learning MMIA now. Thanks for the information.
Is cytospace a good tool to do this too?
Besides microRNA and mRNA, I also have 450K DNA methylation array data from the
same matched samples. Will Partek Genomics Suite integrate all of the data together?
Thanks! |
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h******y
发帖数: 351 | 3 这家公司也在卖水稻表达的人血浆白蛋白。
http://www.amsbio.com/Animal-free-Human-Serum-Albumin-HSA-ecoHS
上几张他们网页上的图给大家看看，行家说说这样的活性算不算好。
Purity and Size of Competitive HSA Products by SDS-PAGE
Figure 1 below shows a Coomassie blue stained gel (left) and a silver
nitrate stained gel (right) comparing size and content of competitive HSA
products. The figure shows that there is no difference in migration patterns
or purity between: 1) ecoHSA™ , 2) a commercial human plasma serum
albumin purchased as a lyophilized ... 阅读全帖 |
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J***2
发帖数: 444 | 4 Scott Blanchard
WEILL CORNELL MEDICAL COLLEGE
Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA
Binding
Paul Driscoll
UNIVERSITY COLLEGE LONDON
Tracking death domain complex assembly with NMR
Qing Fan
COLUMBIA UNIVERSITY
Structural studies of human GABA(B) receptor
Evripidis Gavathiotis
ALBERT EINSTEIN COLLEGE OF MEDICINE
Tracing a Killer's Path: Structural insights into the Activation Pathway of
Pro-Apoptotic BAX
Wayne Hendrickson
COLUMBIA UNIVERSITY
Structural Analysi... 阅读全帖 |
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e*****t
发帖数: 642 | 5 gao ren bu gan
sequencing the whole genome, you could get SNP (for GWAS, linkage analysis).
You could have genetic structure variation, like CNV.
sequencing the mRNA, you will have gene expression data, which could be used
for transcriptome analysis, or eQTL mapping.
Chip-seq gives you DNA-binding proteins analysis, like TF, histone
modification.
bisulfite sequencing give you DNA methylation, which has high correlation
with gene expression. |
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n********t
发帖数: 1079 | 6 这个只是测状态，不是功能，比如methylation也不是直接测功能 |
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s******s
发帖数: 13035 | 7 表达基因TSS前面low met，但是记得基因体是high met的 |
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s******y
发帖数: 28562 | 8 谢谢。再问一个白痴问题啊，你们在96孔板上铺半固体培养基的时候，如何避免
形成弯曲的表面？还是无所谓？还有里面的胶质，是regular agarose, low-melting
point agarose,还是 methyl-cellulose？ |
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j*p
发帖数: 411 | 9 本人在wet lab里面做纯数据分析，for NGS data analysis, 简单介绍一些自己接触过
，并且觉得挺有用的工具，说的有点杂，权作抛砖引玉，还请不吝赐教。
Next-Gen sequencing(NGS)和现在正在发展的3rd-gen sequencing将会在生物学研究中
被越来越广泛应用。不管你信不信，反正我信了。一是基于实验成本的降低（$1k
whole-genome sequencing is coming），越来越多的实验室可以操作；二是可以提供
相对low throughput experiment多的多的数据和信息，可以看到很多从前看不到的东
西；三是sequencer本身对测序的准确性正在逐渐提高，所以实验固有错误率降低；四
是各种算法的成熟应用，这使得很多由于实验产生的误差在出数据后通过对数据的分析
得以过滤。按照library preparation来分，NGS主要有DNA-seq和RNA-seq
DNA-seq is usually used as ChIP-seq to study transcription factor(TF)-DNA
bi... 阅读全帖 |
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j*p
发帖数: 411 | 10 本人在wet lab里面做纯数据分析，for NGS data analysis, 简单介绍一些自己接触过
，并且觉得挺有用的工具，说的有点杂，权作抛砖引玉，还请不吝赐教。
Next-Gen sequencing(NGS)和现在正在发展的3rd-gen sequencing将会在生物学研究中
被越来越广泛应用。不管你信不信，反正我信了。一是基于实验成本的降低（$1k
whole-genome sequencing is coming），越来越多的实验室可以操作；二是可以提供
相对low throughput experiment多的多的数据和信息，可以看到很多从前看不到的东
西；三是sequencer本身对测序的准确性正在逐渐提高，所以实验固有错误率降低；四
是各种算法的成熟应用，这使得很多由于实验产生的误差在出数据后通过对数据的分析
得以过滤。按照library preparation来分，NGS主要有DNA-seq和RNA-seq
DNA-seq is usually used as ChIP-seq to study transcription factor(TF)-DNA
bi... 阅读全帖 |
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s******s
发帖数: 13035 | 11 你的理解正确。就是有/无methylation的区别
05年的paper你还能指望啥？ ChIP-chip，虽然80kb糙了点，不过也过得去了。
analysis |
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s******s
发帖数: 13035 | 15 第一种太糙了，估计其他抗性啥的都不表达了。
你为什么不去问paper的author |
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b**********8
发帖数: 349 | 16 体外甲基化修饰后的质粒是直接用来转染细胞的，不用做转化和质粒抽提，应该不用考
虑抗性丢失的问题了吧？ Anyway， thanks a lot！ |
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b**********8
发帖数: 349 | 17 多谢回复，你提供的信息对我实在太有用了，thanks a lot |
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i*****i
发帖数: 154 | 18 最近老板要从病人的Blood和Urine中提取DNA然后做一个基因的promoter methylation
研究，请问板上有经验的前辈都是用的那个公司的kit？
听说Qiagen的不错，不知道具体的是哪一个？
谢谢 |
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a******g
发帖数: 129 | 19 I haven't done methylation ChIP-seq. For TF ChIP-seq on GAII from illumina,
20m should be fine.
sample. |
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p*****n
发帖数: 68 | 20 anybody can help me finding the following papers. thanks a lot.
Methylated N-(4-N,N-dimethylaminobenzyl) chitosan for novel effective gene
carriers.
Theerasak Rojanarataa,
European Journal of Pharmaceutics and Biopharmaceutics
Volume 70, Issue 1, September 2008, Pages 207-214
Expert Opinion on Drug Delivery
1) Recent developments in nanoparticle-based drug delivery and targeting
systems with emphasis on protein-based nanoparticles
May 2008, Vol. 5, No. 5, Pages 499-515 (doi:10.1517/17425247.5... 阅读全帖 |
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m*******n
发帖数: 387 | 22 谢谢回复
那要是把这个蛋白纯化出来，做质谱如何？
isotope |
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g****e
发帖数: 137 | 23
Yes, it's doable but it's not as sensitive as isotope labeled protein. |
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E********8
发帖数: 22 | 24 possible publication list for people graduated since 2010
118 伊成器
1. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-
associated FTO.
Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, Yi C, Lindahl T, Pan T, Yang YG
, He C.
Nat Chem Biol. 2011 Oct 16;7(12):885-7. doi: 10.1038/nchembio.687.
2.Targeting MgrA-mediated virulence regulation in Staphylococcus aureus.
Sun F, Zhou L, Zhao BC, Deng X, Cho H, Yi C, Jian X, Song CX, Luan CH, Bae T
, Li Z, He C.
Chem Biol. 2011 Aug 26;18(8)... 阅读全帖 |
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A******y
发帖数: 2041 | 25 For number 1, if you are worry about reviewers, you have to do two things: 1
. Mass spec will tell you where the modification is. 2. For your gene of
interest, you can use different but well know histone acetylation or
methylation marker doing chromatin IP. Both require experience and special
training to do them right though. Even if you can find specific actylated
ab for the resiude, reviewers will ask for these two experiments for a good
journal. As for as I know, histone H3 K9 Chip is ve... 阅读全帖 |
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l**********1
发帖数: 5204 | 26 if limited to Methyl transferase, Acetyl transferase,
Protein tyrosine phosphatase to perform a structural prediction of the putative ligands.
The modelling of the domains takes into account the different ligand
orientation when necessary as well as the orientation of the important
residues involved in binding.
Please go to
//adan-embl.ibmc.umh.es/
from
//www.embl.de/
and more pls go to
//mamba.bio.uci.edu/rt95.06.16/rt_1.html
from
//www.mcb.harvard.edu/hastings/dino.html |
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z****u
发帖数: 1007 | 27 比如说，我能通过laser capture microscope分离出几百个stem cell, 几百个TA cell
。啥技术能比较他们的methylation, acetylation 等等的状态。 没做过，不懂。 |
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y******8
发帖数: 1764 | 28 With this tiny amount, only DNA methylation is doable. |
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z****u
发帖数: 1007 | 29 比如说，我能通过laser capture microscope分离出几百个stem cell, 几百个TA cell
。啥技术能比较他们的methylation, acetylation 等等的状态。 没做过，不懂。 |
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y******8
发帖数: 1764 | 30 With this tiny amount, only DNA methylation is doable. |
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l*****1
发帖数: 8 | 31 Need a paper again.
Thank you so much!
Please email to : l*******[email protected]
http://www.ncbi.nlm.nih.gov/pubmed/7956042
DNA methylation, genomic imprinting, and mammalian development.
Li E, Beard C, Forster AC, Bestor TH, Jaenisch R.
SourceMassachusetts General Hospital-East, Cardiovascular Research Center,
Charlestown 02129. |
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O*C
发帖数: 649 | 32 你要看组蛋白上面什么样的变化？methylation, Ub, Ac?还是和dna bind的dynamic？
每个nucleosome里面组蛋白是个octamer，h2a, h2b, h3, h4 X2，外面饶130左右个bp
，你要看那个？ |
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a****d
发帖数: 624 | 33 比如用Illumina genmoe-wide找出几百个有变化的genes之后，如何用什么软件作图，
我找到的有IPA， 但是是要钱的。有什么open sourcer吗？谢谢 |
|
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l**********1
发帖数: 5204 | 35 Sure
plus
04.Jan.12
Postdoctoral position in Plant Epigenetics
The laboratory "Génétique, reproduction et développement" (GReD, CNRS/
Université Clermont Ferrand 1 et 2) is looking for two postdoctoral
researchers to study the molecular bases of epigenetic gene silencing as
part of a project funded by the European Research Council (ERC). The
successful applicants will join a young research group and research projects
aimed at getting a better understanding of the molecular mechanisms
governing D... 阅读全帖 |
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d******u
发帖数: 99 | 36 楼主写的前三位都见过，对他们领域也比较了解。xw，jk早年做forward genetics相当
成功，即便在当今，也很少能见到自己实验室通过筛突变体，能把一整条全新的
pathway都给找出来。xw的cop9 signalsome 通过生化纯化复合体，最后发现每一个亚
基都是之前筛选出来的突变体; jk的sos3-sos2-sos1 一条perfect的盐胁迫通路。两人
近年来都涉足小rna和dna methylation都做得非常好。再说xn对NPR1的工作那也是非常
出色，从NPR1到下游转录因子，在整个水杨酸领域贡献都很大。相比较下jen sheen的
工作全部依靠protoplast，genetics做得不好，data 不够solid，所以影响力自然就小
。 |
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d******u
发帖数: 99 | 37 楼主写的前三位都见过，对他们领域也比较了解。xw，jk早年做forward genetics相当
成功，即便在当今，也很少能见到自己实验室通过筛突变体，能把一整条全新的
pathway都给找出来。xw的cop9 signalsome 通过生化纯化复合体，最后发现每一个亚
基都是之前筛选出来的突变体; jk的sos3-sos2-sos1 一条perfect的盐胁迫通路。两人
近年来都涉足小rna和dna methylation都做得非常好。再说xn对NPR1的工作那也是非常
出色，从NPR1到下游转录因子，在整个水杨酸领域贡献都很大。相比较下jen sheen的
工作全部依靠protoplast，genetics做得不好，data 不够solid，所以影响力自然就小
。 |
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l**********1
发帖数: 5204 | 38 please try DIME if your data set was from ChIP-seq
PURPOSE: R package that considers an ensemble of finite mixture models
combined with a local false discovery rate (fdr) for analyzing ChIP-seq data
comparing two samples. This package can also be used to identify
differential in other high throughput data such as microarray and DNA
methylation.
//www.stat.osu.edu/~statgen/SOFTWARE/DIME/ |
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n********k
发帖数: 2818 | 39 Are u referring to the mRNA bind protein and methylation studies? I thought
they are ok as resource papers...any insider information?
similar
most |
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k**********e
发帖数: 13 | 40 LLS special fellow award 竞争很激烈的，中奖率很低，去年好像只有7％不到。。有
多侧重于translational research的趋势。而且几乎没有neuroscience方向的。。。
actively-funded的中国同胞好像只有两三个：
有兴趣的可以研究研究lls的口味：
check:
http://www.lls.org/#/researchershealthcareprofessionals/academi
Career Development:Special Fellow
Suhua Feng, PhD - 2011 (Active) - 3412-11
Molecular, Cell and Developmental Biology
The Regents of the University of California, Los Angeles
Los Angeles, CA US
Profiling DNA methylation in human cells at single nucleotide resolution
Career D... 阅读全帖 |
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c********r
发帖数: 189 | 41 【 以下文字转载自 Neuroscience 讨论区 】
发信人: coollester (生与死), 信区: Neuroscience
标 题: 神经领域做epigenetics的大牛都有谁啊？
发信站: BBS 未名空间站 (Wed Jun 20 08:44:37 2012, 美东)
各位畅谈一下？我知道的有宋红军，做DNA methylation&neurogenesis |
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j*p
发帖数: 411 | 42 1. 许多癌症的存活率之所以很低，很大一个原因，是相当一部分患者在确诊患癌症的
时候，已经是很晚期。相反，如果发现的早，那么按照现在的医学水平，还是有很多办
法可以治愈或者控制许多癌症，并以此延长患者的生命。
2. NGS以及其他技术（例如cell sorting, signal-cell seq/image）的发展，当然也
包括像TCGA等大型项目的实施，将在不久的将来对癌症的早期诊断获得突破，尽管目前
还存有许多实验上和分析上的技术问题。
3. 然而这些技术的发展对了解癌症机理的贡献，并以此提出新的治疗方案，或者发明
新的药物，短期内不会有太大的突破。不仅仅因为癌症，作为一个笼统的概念，是数百
个不同的疾病的总和，不同的癌症发病机理有可能会非常不同。这里牵涉到的问题非常
多，例如此前有同学说的，signaling pathway，gene and protein expression, post
transcriptional and translational modification等，也涉及到DNA/RNA
methylation，acetylation, histome m... 阅读全帖 |
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s******s
发帖数: 13035 | 43 ft。你这个就是methylation，epigenetics的一小部分。
另外，你这个没有自己做过看文章是看不出的，这玩意儿
很夸张的，sample都是好几ug级别的才够做library, 这个
做cell line不错，做其他的想想要多少细胞吧 |
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y***i
发帖数: 11639 | 44 “肿瘤很可能不会真正依赖于某个或某些个driving mutations上”这个未必成立。有
能力让细胞不断增殖的pathway是有限的。不是什么东西出毛病了，细胞都会变癌症，
既然是有限，就说明肿瘤细胞必然依赖于某些基因的功能。那么干掉这些基因，也就一
定能抑制肿瘤细胞。NGS不是找到这些基因的唯一办法，但肯定是最有力的办法，我觉
得可能是唯一最有力的办法。另外用NGS 研究methylation的工作已经很多了。
有基因没有药，这个当然没办法。只能多实验。 |
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b*******m
发帖数: 3 | 45 【 以下文字转载自 Postdoc 讨论区 】
发信人: bioinform (ngs), 信区: Postdoc
标 题: postdoc position available in bioinformatics
发信站: BBS 未名空间站 (Fri Jul 20 00:44:34 2012, 美东)
Hiring unit:
Garmire Group (PI starting 09/01/2012, the postdoc position available 09/01
or later)
University of Hawaii Cancer Research Center
Job description:
Located on the beautiful sea shore of Honolulu, Hawaii, overlooking the
Pacific Ocean, the University of Hawaii Cancer Center (UHCC) is one of only
66 research organizations in the coun... 阅读全帖 |
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D******9
发帖数: 2665 | 46 突变五花八样， 大多数蛋白在细胞里， 又没有酶活性。 健康人早点测个序， 假如有
这些突
变，早点做个肠镜才是真的。
Comprehensive molecular characterization of human colon and rectal cancer.
Cancer Genome Atlas Network.
Abstract
To characterize somatic alterations in colorectal carcinoma, we conducted a
genome-scale analysis of 276 samples, analysing exome sequence, DNA copy
number, promoter methylation and messenger RNA and microRNA expression. A
subset of these samples (97) underwent low-depth-of-coverage whole-genome
sequencing. In total, 16% of co... 阅读全帖 |
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l**********1
发帖数: 5204 | 47 坏啦 连Nat Commun. 灌水文 2013起 也投稿不了啦
Zhang X and Shang Y et al. (2012)
Nat Commun. 3:712
The tRNA methyltransferase NSun2 stabilizes p16INK⁴ mRNA by
methylating the 3'-untranslated region of p16.
link:
//www.ncbi.nlm.nih.gov/pubmed?term=Shang%20Yongfeng%5BAuthor%5D |
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j*p
发帖数: 411 | 48 我所知道的通过RNAseq来找motif，多数是这2种情况：
1. 两个sample，control／treat，跑两个RNAseq，找differential expressed genes
，拿到这个gene list，问，这些gene有什么共同点，例如，gene promoter有没有已知
的TF 的motif，这样可以至少给出几个candidate TF，可以接下来做故事；或者这些
gene sequence本身有什么motif（如果gene又长又多，技术上很难算，当然我遇到这种
情况较少，或者基本不work）。
2. 两个试验，一个input，一个pull down，例如做RNA methylation，RNA－RNA
interaction，等等，通常这种情况是找出RNA中某些位点，信号enrich over input （
如果没input，就是over nothing）。 问题是，这些enriched sites有没有motif（
sequence similarity）。
请问你是哪种情况，如果都不是，不知道能否把你的问题问的清楚些。 |
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s******y
发帖数: 28562 | 49 我记得前一阵子有人说过用promoter methylation 来控制reporter表达的方法
来测量细胞内部的总体的甲基化活性？ |
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l**********1
发帖数: 5204 | 50 人家各做一个residue 3D
Molecular Modeling 的话 还是可能的
//www.ncbi.nlm.nih.gov/pubmed/22448988
Crystal structures of Bcl-xL with 118 (PDB entry 2YXJ) and 4 were used to
model the binding poses of our designed compounds with Bcl-xL. In the
binding models, the structure of Bcl-xL in complex with 4 was superimposed
on that of Bcl-xL in complex with 1. The core scaffold of 4 then replaced
the 4′-chloro-2-methyl-1,1′-biphenyl group of 1 to generate the initial
binding model, which was then refined by a 1 ns mo... 阅读全帖 |
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