l*****c
发帖数: 17 | 1 是啊，我们研究遗传学，分子生物学包括搞统计的人，不断的创造新的名词来解释以前
不能解释的现象。每个都合理，最后表示都不合理。现在的GWAS研究，根本不能对超出
QTL范畴的生物学有人和解释。
这又回到了50年前的解释了，把所有（大部分）疾病/表型看成是数量性状，用微效多
基因来解释，既然是微效多基因，那当然是有无穷的组合了，比如有40个基因，每个基
因可能有50个突变，然后加上这些突变的组合，大家计算以下这有多少？从应用的角度
，接近无穷吧。最近的一篇NG文章用新方法来处理以前的数据，发现12万个SNP（我望
了具体的数值，反正很大）能解释56%的疾病表型，那是不是需要1百万的SNPs能解释80
%呢？显然还达不到，因为有环境因素在。那在计算这多大上百万SNPs的组合表型呢？
这还是只从SNP出发来解释。大家在建立简单的BLUP模型的时候，能考虑多少互作？
还有大量的CNV, chromosome rearrangement,methylation......,然后还有这些遗传因
素的组合呢？我们在研究这些生物现象的时候，用了太多的determinism的方法，考虑
太少的stocha |
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R****n
发帖数: 708 | 2 恩，老板搞了个NCI funded公司，做癌症早期检测，作临床样品。主要是建立个高灵敏
度的mutation/methylation screening.以前我们实验室有人做过array,Single base
extension和ligation 也就10%的灵敏度。 |
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l******o
发帖数: 3764 | 3 用methylight，Q-MSP这样high-throughput的方法
用restriction enzyme的不要
主要问题是针对Q-MSP的:1)用什么方法做primer design; 2)quality control怎么实行
有大包子 谢谢啦！bow~~~ |
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a**p
发帖数: 49 | 5 immunohistochemistry
with methyl blue as background nissl staining |
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l*h
发帖数: 4124 | 6 白瞎了自称的PI。methyl blue做个屁nissl staining。 |
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y*********1
发帖数: 46 | 7 You can look up Keji Zhao's Cell paper: High-resolution profiling of histone
methylations in the human genome.
H3K4me3 would be a good marker for TSS. |
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c****y
发帖数: 14 | 8 Hi, sinister (@_@),
If the CMV promoter is methylated to inhibit transcription, the protein
should be expressed after treatment with demethylation agent 5'Aza, right?
Can you suggest other good promoter for it? Thanks. |
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k*******s
发帖数: 214 | 9 想分析一下么CpG islands. 请推荐好用的预测软件。谢谢 |
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b********w
发帖数: 37 | 11 Int J Oncol. 2010 May;36(5):1235-41.
Altered DNA methylation is associated with docetaxel resistance in human
breast cancer cells.
Kastl L, Brown I, Schofield AC.
可发到b************[email protected]
Thanks. |
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o********r
发帖数: 775 | 12 以前有那种定点mutagenesis的protocol，用含mutation的primers和high fidality的
polymerase做linear amplification，然后用只切methylated DNA的RE处理，再
transformation。这样以后想怎么用都行。
现在不用这个protocol了？ |
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R****n
发帖数: 708 | 13 请问是不是只要投简历就行了？我本来有个和illumina qPCR system director 有个面
试机会，结果被放鸽子了。
我有DNA mutation and methylation detection 的背景，非常想进入next generation
sequencing这个领域。请问能不能有空聊聊？谢谢 |
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s********l
发帖数: 1195 | 14 能不能展开说说，是在学术上更有发展么？
epigenetics确实有的做，现在测methylation这些技术已经很成熟了，以后应该会更快
更精准了，最关键是还可以做动态测序实时观测就更牛了，呵呵，只是我看文献的理解。
我自己认为这方面的技术发展空间还挺大的，就是不清楚对个人前途的发展影响怎么样。 |
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R****n
发帖数: 708 | 15 DNA methylation做动态的还不行吧，一是bisulfite那一步就很麻烦，用ｍｅｔｈｙｌ
ａｔｉｏｎ ｓｐｅｉｃｉｆｉｃ ｐｒｏｔｅｉｎ也不是准确。
解。
样。 |
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s********l
发帖数: 1195 | 16 you are right, probably not now.
but new techniques like the one developed by pacific sciences claimed to
physically image the real-time inclusion of each base continuously without
any wash and run process, so if methylation or any modification happens at
one spot, or if there's structual variance at some base spot, supposedly
this new machine should be able to detect, I mean, in the near future. :) |
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s******y
发帖数: 28562 | 17 http://www.sciencemag.org/cgi/content/abstract/science.1195298
Published Online October 28, 2010
Science DOI: 10.1126/science.1195298
Science Express Index
Reports
Calcium-Permeable AMPA Receptor Dynamics Mediate Fear Memory Erasure
Roger L. Clem and Richard L. Huganir*
Traumatic fear memories can be inhibited by behavioral therapy or extinction
training in rodent models, but are prone to relapse. Under some conditions,
however, these treatments generate a permanent effect on behavior
sugges... 阅读全帖 |
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e*r
发帖数: 103 | 18 what kind of mutagen did you use? Why do you think there is something
changed in methylation? |
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n********b
发帖数: 27 | 19 There is a Research Associate II position opening in a Genomics-Microarray
Core in a Cancer Center in southern CA-Los Angeles Area. Please send your
resume/CV to o****[email protected], if you are interested
in it. Thanks.
See job descriptions:
Job Descriptions
Research Associate II
Functional Genomics Core
1. Perform bench work related to research projects & services using
different genomic technologies including Affymetrix GeneChip, Agilent, Roche
NimbleGen and Illumina’s HiScanSQ microarray platfo... 阅读全帖 |
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f*********e
发帖数: 1144 | 20 for #4: Variable Modification: met oxidation
Static Modificaiton: cys carboxy-amido-methylation if IAA is used
Other modification should be specified only when the corresponding
enrichment is performed, otherwise many false postive
identifications
will be introduced |
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e*****n
发帖数: 15 | 21 我这个应该是DNA methylome sequencing吧
whole genome 的DNA，用invitrogen的那个methyMiner kit enrich methylated DNA，
但是这个kit上说要根据下游的实验用fragment DNA 和bead incubate
测序那边要300bp的DNA fragment，所以我enrich这步就得要300bp的啊 |
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C*********m
发帖数: 213 | 23
15N HSQC 没有多少峰？那 一维氢谱的methyl区呢？ |
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c*********t
发帖数: 340 | 24 it is quite normal to have consecutive CpGs all methylated... |
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c*********t
发帖数: 340 | 25 话说，虽然pcr-product是很常用的neg control，但是个人觉得它CONVERT不能保证你
看的那个MOLECULE也CONVERT了
看序列中的其它C都CONVERT了，我觉得这里应该是METHYLATION PROTECTION吧
话说其它C都CONVERT，偏偏CpG context的没有，这个概率很小的 |
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C*******e
发帖数: 4348 | 26 rt
买来做tracing dye用
哪里有卖的？
我搜了半天没搜到啊 |
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T**********t
发帖数: 1604 | 28 Sigma Aldrich
Cat # 198080 |
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C*******e
发帖数: 4348 | 29 谢谢ls两位
不知道为啥半个月前我google出来的都是巨贵无比的
做切片染色的那种
sigma上也没有搜到（现在想想都不可思议）
然后今天帖子一发
去sigma就搜到了
自己都汗颜～ |
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t**k
发帖数: 16 | 30 最近发现一个promoter上有一个CpG的G突变到T(我不确定这个CGCG就是transcription
factor的binding site,但是这个CpG的位置就在转录起始点上游大概250bp左右,看chip
-sequencing结果,位置比较像)
我想证明一下,这个可能和甲基化有关,并且有可能影响蛋白表达水平的提高. qPCR显示
表达水平提高了,但是不知道是不是就是这个突变造成的.
哪位老师帮忙设计个可行的办法,我是新手,请大家多多帮忙! |
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s******s
发帖数: 13035 | 31 你先测一下到底有没有甲基化再说吧
transcription
chip |
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c*********t
发帖数: 340 | 32 先做一下bisulfite conversion + pyrosequencing看一下原来的序列是不是甲基化的
，如果本来就没甲基化突变成T不能甲基化也没有影响的，那就是TF Sequence-
specific binding的问题。。如果原来是甲基化的那有可能因为去甲基化导致表达升高 |
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t**k
发帖数: 16 | 33 哈哈,多谢高人指点,看来先知道是否是CpG island 是第一步,如果没有甲基化,就白撤
了,如果原来有甲基化,就还有点希望.
我现在就是觉得甲基化如果在C上,G突变了,好像意思不大吧. |
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t**k
发帖数: 16 | 34 对哈,另一条链就是C了, 看东西看的晕头转向. |
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s******s
发帖数: 13035 | 35 1.另一条链是C
2.不是CpG, DNMT1没法maintain甲级化 |
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b****r
发帖数: 17995 | 36 楼主不要过于激动，promoter啥多态都没有的基因不多
先去网上查查这个是不是人家已经发现的多态吧 |
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M*****n
发帖数: 16729 | 37 这个东东不是跟氯仿差不多嘛?
）我在加州，一张塌塌米床是1200刀。
fumigation， 用的是：
全部用这个东西来消毒/杀虫，包括苹果这类的食物。
宝宝，可能也会经常在床上玩。我本来的想法是以后这张床可以给宝宝睡，因为小孩子
睡硬床比较好。 |
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b******n
发帖数: 492 | 38 最近需要设计probe for southern blotting to screen the founders， 有一些问题
想请教一下各位:
1）如果是用gene probe， 一般多长比较好？ 有人说越长越好， 可是大概是多少呢？
2） 如果用oligo probe， 50 bp 差不多吗？ 需要准备至少两个吗？
3） 我现在有好几个 enzyme only cut once in the transgene，但是其中好几个都可
能blocked or impaired by CG methylation, 是不是最好都avoid?
谢谢了！ |
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s******s
发帖数: 13035 | 39 没做过tm，要么你seq以下看看？
methylated, |
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R****n
发帖数: 708 | 40 you are talking about Methylation Specific-HRM, I assume. Althought you are
using qPCR system, you didn't use a beckman probe to identify the sequence
change. So this is not a qPCR method.
ZymoResearch's kit should be fine. We used their kit a lot. There are some
commercial M or UM DNA standard which have been converted. You can use them
to test your primers.
How do you design your primers? flanking any CpG sites?
If you didn't change primer, I guess that you may have PCR product
contamination i... 阅读全帖 |
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t****t
发帖数: 610 | 41 Thanks. It's Methylation Specific-HRM. I'm studying the same CpG islands,
so primers are all the same.
Primers do flank CpG sites.My primers work.
Even I have PCR product contamination, how it is possible to get a Tm lower
than unmethylated control? I have PCR controls, which are already converted
standard DNA (methy and unmethy). They were fine with the right Tms.
Also, although I'm using the same reagents (kit, buffer,...), last week
there was once that my results were fine. Really got confus... 阅读全帖 |
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r*******e
发帖数: 48 | 42 Two postdoctoral positions are available immediately to study
epigenetic modifications on breast cancer. Exciting research
environment, state-of-the-art equipment and facilities are available.
Mandatory requirements: One position is expected to have expertise
in epigenetics, transcription, and genomic approaches (e.g.
microarray, ChIP-chip, ChIP-Seq/RNA-Seq, chromatin remodeling
assays, or global DNA methylation analysis with clinical samples),
cell culture, biochemical and standard molecular as... 阅读全帖 |
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m***f
发帖数: 1622 | 43
扯淡呢，看看高最近两年发表的文章吧
CELL STEM CELL, JBC, STEM CELL, PNAS，都是很不错的
就这样还不能PROMOTION? 在美国都可以tennure了
1. Wu T., Wang H., He J., Kang L., Jiang Y., Liu J., Zhang Y., Kou
Z., Liu L., Zhang X., Gao S. (2011) Reprogramming of trophoblast stem
cells into pluripotent stem cells by Oct4. Stem Cells 2011 Feb 8.
[Epub ahead of print].
2. Kang L., Wu T., Tao Y., Yuan Y., He J., Zhang Y., Luo T., Kou Z.,
Gao S. (2010) Viable mice produced from 3-factor induced pluripotent
stem (iPS) cells through tetrapl... 阅读全帖 |
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c*****l
发帖数: 297 | 44 Bioinformatics Research Scientist - Computational Biology
Job Title Bioinformatics Research Scientist - Computational
Biology
Department Computational Biology
Job Number 20492
Job Description:
The Bioinformatics Research Scientist in the Computational Biology
Department takes a lead role in data management, data integrity
evaluation, statistical analysis, experimental design, and database
development. Responsible for databases development and provides help for
software and computa... 阅读全帖 |
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m*****i
发帖数: 29 | 45 Keji Zhao's top 3 hottest paper in 2010 seems unknown to all of you guys.
High-resolution profiling of histone methylations in the human genome
[PDF] from bmskorea.co.kr
FindIt@Towson…, DE Schones, Z Wang, G Wei, I Chepelev, K Zhao - Cell, 2007
- Elsevier
Cited by 1271 |
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O******e
发帖数: 4845 | 46 按说这个DNA methylation应该是可逆的吧，说不定再传几代，LoxP sites又给
复原了，呵呵 |
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s******s
发帖数: 13035 | 47 我说这个就是因为听人提起来好像有篇文章说是转gfp进去，然后发现细胞
对GFP无爱，加了很多methylation上去，直接抑制表达了 |
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Z**********g
发帖数: 222 | 48 LoxP sites的methylation很可能是组织特异的吧,就是有些组织能被cre knockout掉,
而有些不能? |
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g**********y
发帖数: 423 | 49 我得到这个数据
CellTypeI CellTypeII CellTypeIII
Hypermethylated 5400 1600 500
Hypomethylated 450 1500 150
用Fisher exact test or chisq test只能说明methyaltion和CellType是相关的。
但是不能表明CellType中的哪种enriched with hyper or hypo-methylation。
显然，CellTypeI中Hypermethylated的数目比较多，要用什么test来说明
CellTypeI is significantly enriched with Hypermethylation。
另外 Is CellTypeII enriched with Hypomethylation?
Thanks!!! |
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j********e
发帖数: 52 | 50 Fisher's test is only for binary 2x2 table, use chisq test to test
association between CellType and methylation.
WITHIN each cell type, use binomial test to test if the cell type is
enriched with hypermethylation. This can be done by either calling test
procedures or by permutation. For example, in R |
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